Cytochrome oxidase I (COI), marqueur mitochondrial utilisé pour le DNA barcoding.
Taxons : Cétacés (Baleines), groupe frère des Cétacés : l’Hippopotame, groupe externe de (Cétacés + Hippopotame) : Pinnipèdes (groupe externe).
##
## Attachement du package : 'ape'
## Les objets suivants sont masqués depuis 'package:seqinr':
##
## as.alignment, consensus
## Le chargement a nécessité le package : Biostrings
## Le chargement a nécessité le package : BiocGenerics
##
## Attachement du package : 'BiocGenerics'
## Les objets suivants sont masqués depuis 'package:stats':
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## IQR, mad, sd, var, xtabs
## Les objets suivants sont masqués depuis 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
## table, tapply, union, unique, unsplit, which.max, which.min
## Le chargement a nécessité le package : S4Vectors
## Le chargement a nécessité le package : stats4
##
## Attachement du package : 'S4Vectors'
## L'objet suivant est masqué depuis 'package:utils':
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## findMatches
## Les objets suivants sont masqués depuis 'package:base':
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## expand.grid, I, unname
## Le chargement a nécessité le package : IRanges
## Le chargement a nécessité le package : XVector
## Le chargement a nécessité le package : GenomeInfoDb
##
## Attachement du package : 'Biostrings'
## L'objet suivant est masqué depuis 'package:ape':
##
## complement
## L'objet suivant est masqué depuis 'package:seqinr':
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## translate
## L'objet suivant est masqué depuis 'package:base':
##
## strsplit
Importer le jeu de sequence “Cetacea COI.txt”
# Conversion de .txt en format .fasta
mySequences <- readDNAStringSet("Cetacea COI.txt", format = "fasta")
# Garder juste les numeros ( GI Number) comme nom pour reduire la taille
names(mySequences) <- sub(".*?(\\d+).*", "\\1", names(mySequences))
Paramètres défaut: Une pénalité entre 16 et 18 sur l’ouverture d’indels Et une pénalité entre 2 et 1 sur leur prolongement
# Aligner avec les paramètres par défaut
mySequences_align = AlignSeqs(mySequences, gapOpening = c(-18,-16), gapExtension = c(-2,-1))
## Determining distance matrix based on shared 9-mers:
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## Time difference of 0.01 secs
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## Clustering into groups by similarity:
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## Aligning Sequences:
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## Time difference of 0.39 secs
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## Iteration 1 of 2:
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## Determining distance matrix based on alignment:
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## Reclustering into groups by similarity:
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## Realigning Sequences:
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## Time difference of 0.14 secs
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## Iteration 2 of 2:
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## Determining distance matrix based on alignment:
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## Reclustering into groups by similarity:
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## Realigning Sequences:
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## Time difference of 0.01 secs
# Calcul des distances
mySequences_align_ape = as.DNAbin(mySequences_align)
mySequences_align_JC = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "JC69")
#Visualisation
plot(mySequences_align_JC, main = "Valeurs de distance entre les séquences par position nucléotidique pour l'alignement avec les paramètres par défaut.", ylab = "distance", xlab= "position")
Pénalités de zéro pour l’ouverture d’indels (gaps) et leur prolongement.
# Aligner avec les paramètres par défaut
mySequences_align_param_zero = AlignSeqs(mySequences, gapOpening = 0, gapExtension = 0 )
## Determining distance matrix based on shared 9-mers:
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## Time difference of 0.01 secs
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## Clustering into groups by similarity:
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## Time difference of 0 secs
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## Aligning Sequences:
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## Time difference of 0.34 secs
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## Iteration 1 of 2:
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## Determining distance matrix based on alignment:
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
## ================================================================================
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## Time difference of 0.01 secs
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## Realigning Sequences:
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## Time difference of 0.31 secs
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## Iteration 2 of 2:
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## Determining distance matrix based on alignment:
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
## ================================================================================
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## Time difference of 0 secs
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## Realigning Sequences:
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## Time difference of 0.16 secs
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## Refining the alignment:
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## Time difference of 0.17 secs
mySequences_align_ape_param_zero = as.DNAbin(mySequences_align_param_zero)
# Calcul des distances
mySequences_align_JC_param_zero = dist.dna(mySequences_align_ape_param_zero, pairwise.deletion = FALSE, model = "JC69")
#Visualisation
plot(mySequences_align_JC_param_zero, main = "Valeurs de distance entre les séquences par position nucléotidique", ylab = "distance", xlab= "position")
head(GENETIC_CODE_TABLE)
## name
## 1 Standard
## 2 Vertebrate Mitochondrial
## 3 Yeast Mitochondrial
## 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
## 5 Invertebrate Mitochondrial
## 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
## name2 id AAs
## 1 SGC0 1 FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## 2 SGC1 2 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
## 3 SGC2 3 FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## 4 SGC3 4 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## 5 SGC4 5 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
## 6 SGC5 6 FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## Starts
## 1 ---M---------------M---------------M----------------------------
## 2 --------------------------------MMMM---------------M------------
## 3 ----------------------------------MM----------------------------
## 4 --MM---------------M------------MMMM---------------M------------
## 5 ---M----------------------------MMMM---------------M------------
## 6 -----------------------------------M----------------------------
Paramètres GeneticCode : 2 (Vertebrate Mitochondrial)
my_g_table <- getGeneticCode("2") ## Vertebrate Mitochondrial
mySequences_align_aa = AlignTranslation(
mySequences,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
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## Time difference of 0 secs
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## Clustering into groups by similarity:
## ================================================================================
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## Time difference of 0 secs
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## Aligning Sequences:
## ================================================================================
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## Time difference of 0.06 secs
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## Iteration 1 of 2:
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## Determining distance matrix based on alignment:
## ================================================================================
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
## ================================================================================
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## Time difference of 0 secs
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## Realigning Sequences:
## ================================================================================
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## Time difference of 0.05 secs
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## Alignment converged - skipping remaining iteration.
Cadre de lecture 1:
mySequences_align_aa_cadre_1 = AlignTranslation(
mySequences,
sense = "+",
readingFrame = 1,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
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## Time difference of 0 secs
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## Clustering into groups by similarity:
## ================================================================================
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## Time difference of 0 secs
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## Aligning Sequences:
## ================================================================================
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## Time difference of 0.06 secs
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## Iteration 1 of 2:
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## Determining distance matrix based on alignment:
## ================================================================================
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
## ================================================================================
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## Time difference of 0 secs
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## Realigning Sequences:
## ================================================================================
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## Time difference of 0.06 secs
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## Iteration 2 of 2:
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## Determining distance matrix based on alignment:
## ================================================================================
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
## ================================================================================
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## Time difference of 0 secs
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## Realigning Sequences:
## ================================================================================
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## Time difference of 0.01 secs
# Conversion pour format ape
mySequences_align_ape = as.DNAbin(mySequences_align)
Matrice de distances
# Jukes et Cantor
mySequences_align_JC = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "JC69")
# Kimura 2 paramètres
mySequences_align_K80 = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "K80")
# Tamura et Nei
mySequences_align_TN93 = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "TN93")
# Galtier et Gouy
mySequences_align_GG95 = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "GG95")
Visualisations
plot(mySequences_align_JC, main = "Valeurs de distance entre les séquences par position nucléotidique pour Jukes et Cantor", ylab = "distance", xlab= "position")
plot(mySequences_align_K80, main = "Valeurs de distance entre les séquences par position nucléotidique pour Kimura 2 paramètres", ylab = "distance", xlab= "position")
plot(mySequences_align_TN93, main = "Valeurs de distance entre les séquences par position nucléotidique pour Tamura et Nei", ylab = "distance", xlab= "position")
plot(mySequences_align_GG95, main = "Valeurs de distance entre les séquences par position nucléotidique pour Galtier et Gouy", ylab = "distance", xlab= "position")
Construction d’arbres avec le Neighbor-Joining
mySequences_align_JC_NJ = nj(mySequences_align_JC)
mySequences_align_K80_NJ = nj(mySequences_align_K80)
mySequences_align_TN93_NJ = nj(mySequences_align_TN93)
mySequences_align_GG95_NJ = nj(mySequences_align_GG95)
Arbres phylogénétiques
plot(mySequences_align_JC_NJ, main="Jukes et Cantor")
plot(mySequences_align_K80_NJ, main="Kimura 2 parametres 1980")
plot(mySequences_align_TN93_NJ, main="Tamura et Nei 1993")
plot(mySequences_align_GG95_NJ, main="Galtier and Gouy 1995")
Comparaison des modèles entre eux par corrélation (Pearson)
round(cor(cbind(mySequences_align_JC,mySequences_align_TN93,mySequences_align_K80, mySequences_align_GG95)),3)
## mySequences_align_JC mySequences_align_TN93
## mySequences_align_JC 1.000 0.998
## mySequences_align_TN93 0.998 1.000
## mySequences_align_K80 0.999 0.999
## mySequences_align_GG95 0.866 0.840
## mySequences_align_K80 mySequences_align_GG95
## mySequences_align_JC 0.999 0.866
## mySequences_align_TN93 0.999 0.840
## mySequences_align_K80 1.000 0.850
## mySequences_align_GG95 0.850 1.000
Analyse Bootstrap
mySequences_align_JC_NJ_boot = boot.phylo(phy = mySequences_align_JC_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "JC69")), B = 1000)
## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.
mySequences_align_TN_NJ_boot = boot.phylo(phy = mySequences_align_TN93_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "TN93")), B = 1000)
## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.
mySequences_align_K80_NJ_boot = boot.phylo(phy = mySequences_align_K80_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "K80")), B = 1000)
## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.
mySequences_align_GG95_NJ_boot = boot.phylo(phy = mySequences_align_GG95_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "GG95")), B = 1000)
## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.
Arbres Bootstrap
plot(mySequences_align_JC_NJ, main = "Jukes et Cantor", no.margin = TRUE)
nodelabels(mySequences_align_JC_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
plot(mySequences_align_TN93_NJ, main = "Tamura et Nei 1993", no.margin = TRUE)
nodelabels(mySequences_align_TN_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
plot(mySequences_align_K80_NJ, main = "Kimura 2 parametres 1980", no.margin = TRUE)
nodelabels(mySequences_align_K80_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
plot(mySequences_align_GG95_NJ, main = "GG95", no.margin = TRUE)
nodelabels(mySequences_align_GG95_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
Comparaison des Bootstraps
#Enlever les NA pour ne pas avoir d'erreur
mySequences_align_JC_NJ_boot <- na.omit(mySequences_align_JC_NJ_boot)
mySequences_align_TN_NJ_boot <- na.omit(mySequences_align_TN_NJ_boot)
mySequences_align_K80_NJ_boot <- na.omit(mySequences_align_K80_NJ_boot)
mySequences_align_GG95_NJ_boot <- na.omit(mySequences_align_GG95_NJ_boot)
round(cor(cbind(mySequences_align_JC_NJ_boot,mySequences_align_TN_NJ_boot,mySequences_align_K80_NJ_boot, mySequences_align_GG95_NJ_boot)),3)
## mySequences_align_JC_NJ_boot
## mySequences_align_JC_NJ_boot 1.000
## mySequences_align_TN_NJ_boot 0.634
## mySequences_align_K80_NJ_boot 0.675
## mySequences_align_GG95_NJ_boot 0.238
## mySequences_align_TN_NJ_boot
## mySequences_align_JC_NJ_boot 0.634
## mySequences_align_TN_NJ_boot 1.000
## mySequences_align_K80_NJ_boot 0.818
## mySequences_align_GG95_NJ_boot 0.603
## mySequences_align_K80_NJ_boot
## mySequences_align_JC_NJ_boot 0.675
## mySequences_align_TN_NJ_boot 0.818
## mySequences_align_K80_NJ_boot 1.000
## mySequences_align_GG95_NJ_boot 0.458
## mySequences_align_GG95_NJ_boot
## mySequences_align_JC_NJ_boot 0.238
## mySequences_align_TN_NJ_boot 0.603
## mySequences_align_K80_NJ_boot 0.458
## mySequences_align_GG95_NJ_boot 1.000
Rechercher le meilleur modèle
mySequences_phangorn = as.phyDat(mySequences_align_ape)
mySequences_modelTest = phangorn::modelTest(mySequences_phangorn)
## Model df logLik AIC BIC
## JC 61 -6699.334 13520.67 13846.62
## JC+I 62 -6343.549 12811.1 13142.39
## JC+G(4) 62 -6353.09 12830.18 13161.47
## JC+G(4)+I 63 -6340.357 12806.71 13143.35
## F81 64 -6638.961 13405.92 13747.9
## F81+I 65 -6267.654 12665.31 13012.63
## F81+G(4) 65 -6275.782 12681.56 13028.89
## F81+G(4)+I 66 -6263.407 12658.81 13011.48
## K80 62 -6335.641 12795.28 13126.57
## K80+I 63 -5925.895 11977.79 12314.43
## K80+G(4) 63 -5917.566 11961.13 12297.77
## K80+G(4)+I 64 -5910.923 11949.85 12291.82
## HKY 65 -6276.194 12682.39 13029.71
## HKY+I 66 -5834.262 11800.52 12153.19
## HKY+G(4) 66 -5830.95 11793.9 12146.57
## HKY+G(4)+I 67 -5823.406 11780.81 12138.82
## TrNe 63 -6296.975 12719.95 13056.59
## TrNe+I 64 -5887.889 11903.78 12245.76
## TrNe+G(4) 64 -5890.955 11909.91 12251.89
## TrNe+G(4)+I 65 -5877.541 11885.08 12232.41
## TrN 66 -6263.725 12659.45 13012.12
## TrN+I 67 -5829.366 11792.73 12150.74
## TrN+G(4) 67 -5827.718 11789.44 12147.45
## TrN+G(4)+I 68 -5818.456 11772.91 12136.27
## TPM1 63 -6335.602 12797.2 13133.84
## TPM1+I 64 -5925.7 11979.4 12321.38
## TPM1+G(4) 64 -5917.427 11962.85 12304.83
## TPM1+G(4)+I 65 -5910.598 11951.2 12298.52
## K81 63 -6335.602 12797.2 13133.84
## K81+I 64 -5925.7 11979.4 12321.38
## K81+G(4) 64 -5917.427 11962.85 12304.83
## K81+G(4)+I 65 -5910.598 11951.2 12298.52
## TPM1u 66 -6276.094 12684.19 13036.85
## TPM1u+I 67 -5833.82 11801.64 12159.65
## TPM1u+G(4) 67 -5830.683 11795.37 12153.38
## TPM1u+G(4)+I 68 -5822.876 11781.75 12145.11
## TPM2 63 -6275.356 12676.71 13013.35
## TPM2+I 64 -5900.296 11928.59 12270.57
## TPM2+G(4) 64 -5889.941 11907.88 12249.86
## TPM2+G(4)+I 65 -5881.346 11892.69 12240.01
## TPM2u 66 -6234.278 12600.56 12953.22
## TPM2u+I 67 -5824.232 11782.46 12140.47
## TPM2u+G(4) 67 -5821.934 11777.87 12135.88
## TPM2u+G(4)+I 68 -5812.364 11760.73 12124.08
## TPM3 63 -6335.582 12797.16 13133.8
## TPM3+I 64 -5922.373 11972.75 12314.73
## TPM3+G(4) 64 -5915.104 11958.21 12300.19
## TPM3+G(4)+I 65 -5907.827 11945.65 12292.98
## TPM3u 66 -6276.022 12684.04 13036.71
## TPM3u+I 67 -5830.507 11795.01 12153.02
## TPM3u+G(4) 67 -5828.685 11791.37 12149.38
## TPM3u+G(4)+I 68 -5820.253 11776.51 12139.86
## TIM1e 64 -6296.938 12721.88 13063.86
## TIM1e+I 65 -5887.793 11905.59 12252.91
## TIM1e+G(4) 65 -5890.803 11911.61 12258.93
## TIM1e+G(4)+I 66 -5877.297 11886.59 12239.26
## TIM1 67 -6263.631 12661.26 13019.27
## TIM1+I 68 -5828.973 11793.95 12157.3
## TIM1+G(4) 68 -5827.429 11790.86 12154.21
## TIM1+G(4)+I 69 -5817.935 11773.87 12142.57
## TIM2e 64 -6237.587 12603.17 12945.15
## TIM2e+I 65 -5853.553 11837.11 12184.43
## TIM2e+G(4) 65 -5859.192 11848.38 12195.71
## TIM2e+G(4)+I 66 -5843.839 11819.68 12172.34
## TIM2 67 -6222.408 12578.82 12936.83
## TIM2+I 68 -5816.425 11768.85 12132.2
## TIM2+G(4) 68 -5816.814 11769.63 12132.98
## TIM2+G(4)+I 69 -5805.14 11748.28 12116.98
## TIM3e 64 -6296.937 12721.87 13063.85
## TIM3e+I 65 -5883.586 11897.17 12244.49
## TIM3e+G(4) 65 -5888.332 11906.66 12253.99
## TIM3e+G(4)+I 66 -5873.437 11878.87 12231.54
## TIM3 67 -6263.573 12661.15 13019.16
## TIM3+I 68 -5825.501 11787 12150.36
## TIM3+G(4) 68 -5825.397 11786.79 12150.15
## TIM3+G(4)+I 69 -5814.993 11767.99 12136.68
## TVMe 65 -6275.16 12680.32 13027.64
## TVMe+I 66 -5896.951 11925.9 12278.57
## TVMe+G(4) 66 -5887.499 11907 12259.66
## TVMe+G(4)+I 67 -5878.736 11891.47 12249.48
## TVM 68 -6233.969 12603.94 12967.29
## TVM+I 69 -5820.188 11778.38 12147.07
## TVM+G(4) 69 -5819.268 11776.54 12145.23
## TVM+G(4)+I 70 -5808.999 11758 12132.04
## SYM 66 -6237.48 12606.96 12959.63
## SYM+I 67 -5848.96 11831.92 12189.93
## SYM+G(4) 67 -5856.016 11846.03 12204.04
## SYM+G(4)+I 68 -5839.587 11815.17 12178.53
## GTR 69 -6222.154 12582.31 12951
## GTR+I 70 -5812.051 11764.1 12138.14
## GTR+G(4) 70 -5813.937 11767.87 12141.91
## GTR+G(4)+I 71 -5801.327 11744.65 12124.04
env <- attr(mySequences_modelTest, "env")
ls(env=env)
## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"
#Meilleur modele avec les parametre AIC et BIC.
mySequences_modelTest[order(mySequences_modelTest$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 71 -5801.327 11744.65 8.585027e-01 11751.59 8.330917e-01
## 68 TIM2+G(4)+I 69 -5805.140 11748.28 1.400575e-01 11754.82 1.653002e-01
## 84 TVM+G(4)+I 70 -5808.999 11758.00 1.086518e-03 11764.74 1.163642e-03
## 44 TPM2u+G(4)+I 68 -5812.364 11760.73 2.774303e-04 11767.08 3.602968e-04
## 90 GTR+I 70 -5812.051 11764.10 5.133160e-05 11770.84 5.497525e-05
## 91 GTR+G(4) 70 -5813.937 11767.87 7.784852e-06 11774.61 8.337440e-06
## 76 TIM3+G(4)+I 69 -5814.993 11767.99 7.362056e-06 11774.53 8.688927e-06
## 66 TIM2+I 68 -5816.425 11768.85 4.780728e-06 11775.20 6.208698e-06
## 67 TIM2+G(4) 68 -5816.814 11769.63 3.239588e-06 11775.98 4.207231e-06
## 24 TrN+G(4)+I 68 -5818.456 11772.91 6.269809e-07 11779.27 8.142557e-07
## 60 TIM1+G(4)+I 69 -5817.935 11773.87 3.886606e-07 11780.41 4.587093e-07
## 52 TPM3u+G(4)+I 68 -5820.253 11776.51 1.039606e-07 11782.86 1.350129e-07
## 83 TVM+G(4) 69 -5819.268 11776.54 1.024807e-07 11783.08 1.209509e-07
## 43 TPM2u+G(4) 67 -5821.934 11777.87 5.260518e-08 11784.03 7.506381e-08
## 82 TVM+I 69 -5820.188 11778.38 4.083387e-08 11784.92 4.819340e-08
## 16 HKY+G(4)+I 67 -5823.406 11780.81 1.208125e-08 11786.98 1.723908e-08
## 36 TPM1u+G(4)+I 68 -5822.876 11781.75 7.545176e-09 11788.11 9.798867e-09
## 42 TPM2u+I 67 -5824.232 11782.46 5.287646e-09 11788.63 7.545090e-09
## 75 TIM3+G(4) 68 -5825.397 11786.79 6.068114e-10 11793.15 7.880617e-10
## 74 TIM3+I 68 -5825.501 11787.00 5.465109e-10 11793.36 7.097499e-10
## 23 TrN+G(4) 67 -5827.718 11789.44 1.619205e-10 11795.60 2.310489e-10
## 59 TIM1+G(4) 68 -5827.429 11790.86 7.955656e-11 11797.21 1.033195e-10
## 51 TPM3u+G(4) 67 -5828.685 11791.37 6.155710e-11 11797.54 8.783756e-11
## 22 TrN+I 67 -5829.366 11792.73 3.114656e-11 11798.90 4.444390e-11
## 15 HKY+G(4) 66 -5830.950 11793.90 1.738266e-11 11799.88 2.721267e-11
## 58 TIM1+I 68 -5828.973 11793.95 1.698083e-11 11800.30 2.205289e-11
## 50 TPM3u+I 67 -5830.507 11795.01 9.954726e-12 11801.18 1.420468e-11
## 35 TPM1u+G(4) 67 -5830.683 11795.37 8.345047e-12 11801.53 1.190778e-11
## 14 HKY+I 66 -5834.262 11800.52 6.333259e-13 11806.50 9.914763e-13
## 34 TPM1u+I 67 -5833.820 11801.64 3.622694e-13 11807.81 5.169324e-13
## 88 SYM+G(4)+I 68 -5839.587 11815.17 4.172462e-16 11821.53 5.418747e-16
## 64 TIM2e+G(4)+I 66 -5843.839 11819.68 4.386452e-17 11825.66 6.867023e-17
## 86 SYM+I 67 -5848.960 11831.92 9.635430e-20 11838.09 1.374907e-19
## 62 TIM2e+I 65 -5853.553 11837.11 7.205475e-21 11842.90 1.235747e-20
## 87 SYM+G(4) 67 -5856.016 11846.03 8.311607e-23 11852.20 1.186007e-22
## 63 TIM2e+G(4) 65 -5859.192 11848.38 2.563529e-23 11854.18 4.396479e-23
## 72 TIM3e+G(4)+I 66 -5873.437 11878.87 6.141221e-30 11884.85 9.614126e-30
## 20 TrNe+G(4)+I 65 -5877.541 11885.08 2.752968e-31 11890.88 4.721370e-31
## 56 TIM1e+G(4)+I 66 -5877.297 11886.59 1.292875e-31 11892.57 2.024005e-31
## 80 TVMe+G(4)+I 67 -5878.736 11891.47 1.128095e-32 11897.64 1.609710e-32
## 40 TPM2+G(4)+I 65 -5881.346 11892.69 6.130644e-33 11898.49 1.051412e-32
## 70 TIM3e+I 65 -5883.586 11897.17 6.526699e-34 11902.97 1.119336e-33
## 18 TrNe+I 64 -5887.889 11903.78 2.399054e-35 11909.40 4.500685e-35
## 54 TIM1e+I 65 -5887.793 11905.59 9.720375e-36 11911.38 1.667055e-35
## 71 TIM3e+G(4) 65 -5888.332 11906.66 5.668745e-36 11912.46 9.721958e-36
## 79 TVMe+G(4) 66 -5887.499 11907.00 4.796991e-36 11912.98 7.509724e-36
## 39 TPM2+G(4) 64 -5889.941 11907.88 3.082044e-36 11913.50 5.781991e-36
## 19 TrNe+G(4) 64 -5890.955 11909.91 1.118053e-36 11915.53 2.097494e-36
## 55 TIM1e+G(4) 65 -5890.803 11911.61 4.789756e-37 11917.40 8.214482e-37
## 78 TVMe+I 66 -5896.951 11925.90 3.766415e-40 11931.88 5.896351e-40
## 38 TPM2+I 64 -5900.296 11928.59 9.816867e-41 11934.21 1.841668e-40
## 48 TPM3+G(4)+I 65 -5907.827 11945.65 1.935412e-44 11951.45 3.319252e-44
## 12 K80+G(4)+I 64 -5910.923 11949.85 2.381127e-45 11955.46 4.467054e-45
## 28 TPM1+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 32 K81+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 47 TPM3+G(4) 64 -5915.104 11958.21 3.637865e-47 11963.83 6.824725e-47
## 11 K80+G(4) 63 -5917.566 11961.13 8.427996e-48 11966.57 1.727014e-47
## 27 TPM1+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 31 K81+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 46 TPM3+I 64 -5922.373 11972.75 2.534994e-50 11978.36 4.755711e-50
## 10 K80+I 63 -5925.895 11977.79 2.036060e-51 11983.23 4.172171e-51
## 26 TPM1+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 30 K81+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 65 TIM2 67 -6222.408 12578.82 6.271235e-182 12584.98 8.948601e-182
## 89 GTR 69 -6222.154 12582.31 1.094453e-182 12588.85 1.291708e-182
## 41 TPM2u 66 -6234.278 12600.56 1.193748e-186 12606.54 1.868821e-186
## 61 TIM2e 64 -6237.587 12603.17 3.224702e-187 12608.79 6.049620e-187
## 81 TVM 68 -6233.969 12603.94 2.199107e-187 12610.29 2.855964e-187
## 85 SYM 66 -6237.480 12606.96 4.853013e-188 12612.94 7.597426e-188
## 8 F81+G(4)+I 66 -6263.407 12658.81 2.668370e-199 12664.79 4.177352e-199
## 21 TrN 66 -6263.725 12659.45 1.941635e-199 12665.43 3.039643e-199
## 73 TIM3 67 -6263.573 12661.15 8.311045e-200 12667.31 1.185926e-199
## 57 TIM1 67 -6263.631 12661.26 7.847574e-200 12667.43 1.119792e-199
## 6 F81+I 65 -6267.654 12665.31 1.037730e-200 12671.11 1.779718e-200
## 37 TPM2 63 -6275.356 12676.71 3.463739e-203 12682.15 7.097685e-203
## 77 TVMe 65 -6275.160 12680.32 5.706693e-204 12686.12 9.787040e-204
## 7 F81+G(4) 65 -6275.782 12681.56 3.061432e-204 12687.36 5.250389e-204
## 13 HKY 65 -6276.194 12682.39 2.027638e-204 12688.19 3.477420e-204
## 49 TPM3u 66 -6276.022 12684.04 8.867070e-205 12690.02 1.388146e-204
## 33 TPM1u 66 -6276.094 12684.19 8.243967e-205 12690.17 1.290599e-204
## 17 TrNe 63 -6296.975 12719.95 1.414288e-212 12725.39 2.898075e-212
## 69 TIM3e 64 -6296.937 12721.87 5.407528e-213 12727.49 1.014466e-212
## 53 TIM1e 64 -6296.938 12721.88 5.400399e-213 12727.49 1.013128e-212
## 9 K80 62 -6335.641 12795.28 6.202376e-229 12800.55 1.386198e-228
## 45 TPM3 63 -6335.582 12797.16 2.419369e-229 12802.61 4.957626e-229
## 25 TPM1 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 29 K81 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 4 JC+G(4)+I 63 -6340.357 12806.71 2.043113e-231 12812.15 4.186625e-231
## 2 JC+I 62 -6343.549 12811.10 2.280315e-232 12816.37 5.096384e-232
## 3 JC+G(4) 62 -6353.090 12830.18 1.639507e-236 12835.45 3.664211e-236
## 5 F81 64 -6638.961 13405.92 0.000000e+00 13411.54 0.000000e+00
## 1 JC 61 -6699.334 13520.67 0.000000e+00 13525.77 0.000000e+00
## BIC
## 92 12124.04
## 68 12116.98
## 84 12132.04
## 44 12124.08
## 90 12138.14
## 91 12141.91
## 76 12136.68
## 66 12132.20
## 67 12132.98
## 24 12136.27
## 60 12142.57
## 52 12139.86
## 83 12145.23
## 43 12135.88
## 82 12147.07
## 16 12138.82
## 36 12145.11
## 42 12140.47
## 75 12150.15
## 74 12150.36
## 23 12147.45
## 59 12154.21
## 51 12149.38
## 22 12150.74
## 15 12146.57
## 58 12157.30
## 50 12153.02
## 35 12153.38
## 14 12153.19
## 34 12159.65
## 88 12178.53
## 64 12172.34
## 86 12189.93
## 62 12184.43
## 87 12204.04
## 63 12195.71
## 72 12231.54
## 20 12232.41
## 56 12239.26
## 80 12249.48
## 40 12240.01
## 70 12244.49
## 18 12245.76
## 54 12252.91
## 71 12253.99
## 79 12259.66
## 39 12249.86
## 19 12251.89
## 55 12258.93
## 78 12278.57
## 38 12270.57
## 48 12292.98
## 12 12291.82
## 28 12298.52
## 32 12298.52
## 47 12300.19
## 11 12297.77
## 27 12304.83
## 31 12304.83
## 46 12314.73
## 10 12314.43
## 26 12321.38
## 30 12321.38
## 65 12936.83
## 89 12951.00
## 41 12953.22
## 61 12945.15
## 81 12967.29
## 85 12959.63
## 8 13011.48
## 21 13012.12
## 73 13019.16
## 57 13019.27
## 6 13012.63
## 37 13013.35
## 77 13027.64
## 7 13028.89
## 13 13029.71
## 49 13036.71
## 33 13036.85
## 17 13056.59
## 69 13063.85
## 53 13063.86
## 9 13126.57
## 45 13133.80
## 25 13133.84
## 29 13133.84
## 4 13143.35
## 2 13142.39
## 3 13161.47
## 5 13747.90
## 1 13846.62
mySequences_modelTest[order(mySequences_modelTest$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 68 TIM2+G(4)+I 69 -5805.140 11748.28 1.400575e-01 11754.82 1.653002e-01
## 92 GTR+G(4)+I 71 -5801.327 11744.65 8.585027e-01 11751.59 8.330917e-01
## 44 TPM2u+G(4)+I 68 -5812.364 11760.73 2.774303e-04 11767.08 3.602968e-04
## 84 TVM+G(4)+I 70 -5808.999 11758.00 1.086518e-03 11764.74 1.163642e-03
## 66 TIM2+I 68 -5816.425 11768.85 4.780728e-06 11775.20 6.208698e-06
## 67 TIM2+G(4) 68 -5816.814 11769.63 3.239588e-06 11775.98 4.207231e-06
## 43 TPM2u+G(4) 67 -5821.934 11777.87 5.260518e-08 11784.03 7.506381e-08
## 24 TrN+G(4)+I 68 -5818.456 11772.91 6.269809e-07 11779.27 8.142557e-07
## 76 TIM3+G(4)+I 69 -5814.993 11767.99 7.362056e-06 11774.53 8.688927e-06
## 90 GTR+I 70 -5812.051 11764.10 5.133160e-05 11770.84 5.497525e-05
## 16 HKY+G(4)+I 67 -5823.406 11780.81 1.208125e-08 11786.98 1.723908e-08
## 52 TPM3u+G(4)+I 68 -5820.253 11776.51 1.039606e-07 11782.86 1.350129e-07
## 42 TPM2u+I 67 -5824.232 11782.46 5.287646e-09 11788.63 7.545090e-09
## 91 GTR+G(4) 70 -5813.937 11767.87 7.784852e-06 11774.61 8.337440e-06
## 60 TIM1+G(4)+I 69 -5817.935 11773.87 3.886606e-07 11780.41 4.587093e-07
## 36 TPM1u+G(4)+I 68 -5822.876 11781.75 7.545176e-09 11788.11 9.798867e-09
## 83 TVM+G(4) 69 -5819.268 11776.54 1.024807e-07 11783.08 1.209509e-07
## 15 HKY+G(4) 66 -5830.950 11793.90 1.738266e-11 11799.88 2.721267e-11
## 82 TVM+I 69 -5820.188 11778.38 4.083387e-08 11784.92 4.819340e-08
## 23 TrN+G(4) 67 -5827.718 11789.44 1.619205e-10 11795.60 2.310489e-10
## 51 TPM3u+G(4) 67 -5828.685 11791.37 6.155710e-11 11797.54 8.783756e-11
## 75 TIM3+G(4) 68 -5825.397 11786.79 6.068114e-10 11793.15 7.880617e-10
## 74 TIM3+I 68 -5825.501 11787.00 5.465109e-10 11793.36 7.097499e-10
## 22 TrN+I 67 -5829.366 11792.73 3.114656e-11 11798.90 4.444390e-11
## 50 TPM3u+I 67 -5830.507 11795.01 9.954726e-12 11801.18 1.420468e-11
## 14 HKY+I 66 -5834.262 11800.52 6.333259e-13 11806.50 9.914763e-13
## 35 TPM1u+G(4) 67 -5830.683 11795.37 8.345047e-12 11801.53 1.190778e-11
## 59 TIM1+G(4) 68 -5827.429 11790.86 7.955656e-11 11797.21 1.033195e-10
## 58 TIM1+I 68 -5828.973 11793.95 1.698083e-11 11800.30 2.205289e-11
## 34 TPM1u+I 67 -5833.820 11801.64 3.622694e-13 11807.81 5.169324e-13
## 64 TIM2e+G(4)+I 66 -5843.839 11819.68 4.386452e-17 11825.66 6.867023e-17
## 88 SYM+G(4)+I 68 -5839.587 11815.17 4.172462e-16 11821.53 5.418747e-16
## 62 TIM2e+I 65 -5853.553 11837.11 7.205475e-21 11842.90 1.235747e-20
## 86 SYM+I 67 -5848.960 11831.92 9.635430e-20 11838.09 1.374907e-19
## 63 TIM2e+G(4) 65 -5859.192 11848.38 2.563529e-23 11854.18 4.396479e-23
## 87 SYM+G(4) 67 -5856.016 11846.03 8.311607e-23 11852.20 1.186007e-22
## 72 TIM3e+G(4)+I 66 -5873.437 11878.87 6.141221e-30 11884.85 9.614126e-30
## 20 TrNe+G(4)+I 65 -5877.541 11885.08 2.752968e-31 11890.88 4.721370e-31
## 56 TIM1e+G(4)+I 66 -5877.297 11886.59 1.292875e-31 11892.57 2.024005e-31
## 40 TPM2+G(4)+I 65 -5881.346 11892.69 6.130644e-33 11898.49 1.051412e-32
## 70 TIM3e+I 65 -5883.586 11897.17 6.526699e-34 11902.97 1.119336e-33
## 18 TrNe+I 64 -5887.889 11903.78 2.399054e-35 11909.40 4.500685e-35
## 80 TVMe+G(4)+I 67 -5878.736 11891.47 1.128095e-32 11897.64 1.609710e-32
## 39 TPM2+G(4) 64 -5889.941 11907.88 3.082044e-36 11913.50 5.781991e-36
## 19 TrNe+G(4) 64 -5890.955 11909.91 1.118053e-36 11915.53 2.097494e-36
## 54 TIM1e+I 65 -5887.793 11905.59 9.720375e-36 11911.38 1.667055e-35
## 71 TIM3e+G(4) 65 -5888.332 11906.66 5.668745e-36 11912.46 9.721958e-36
## 55 TIM1e+G(4) 65 -5890.803 11911.61 4.789756e-37 11917.40 8.214482e-37
## 79 TVMe+G(4) 66 -5887.499 11907.00 4.796991e-36 11912.98 7.509724e-36
## 38 TPM2+I 64 -5900.296 11928.59 9.816867e-41 11934.21 1.841668e-40
## 78 TVMe+I 66 -5896.951 11925.90 3.766415e-40 11931.88 5.896351e-40
## 12 K80+G(4)+I 64 -5910.923 11949.85 2.381127e-45 11955.46 4.467054e-45
## 48 TPM3+G(4)+I 65 -5907.827 11945.65 1.935412e-44 11951.45 3.319252e-44
## 11 K80+G(4) 63 -5917.566 11961.13 8.427996e-48 11966.57 1.727014e-47
## 28 TPM1+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 32 K81+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 47 TPM3+G(4) 64 -5915.104 11958.21 3.637865e-47 11963.83 6.824725e-47
## 27 TPM1+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 31 K81+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 10 K80+I 63 -5925.895 11977.79 2.036060e-51 11983.23 4.172171e-51
## 46 TPM3+I 64 -5922.373 11972.75 2.534994e-50 11978.36 4.755711e-50
## 26 TPM1+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 30 K81+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 65 TIM2 67 -6222.408 12578.82 6.271235e-182 12584.98 8.948601e-182
## 61 TIM2e 64 -6237.587 12603.17 3.224702e-187 12608.79 6.049620e-187
## 89 GTR 69 -6222.154 12582.31 1.094453e-182 12588.85 1.291708e-182
## 41 TPM2u 66 -6234.278 12600.56 1.193748e-186 12606.54 1.868821e-186
## 85 SYM 66 -6237.480 12606.96 4.853013e-188 12612.94 7.597426e-188
## 81 TVM 68 -6233.969 12603.94 2.199107e-187 12610.29 2.855964e-187
## 8 F81+G(4)+I 66 -6263.407 12658.81 2.668370e-199 12664.79 4.177352e-199
## 21 TrN 66 -6263.725 12659.45 1.941635e-199 12665.43 3.039643e-199
## 6 F81+I 65 -6267.654 12665.31 1.037730e-200 12671.11 1.779718e-200
## 37 TPM2 63 -6275.356 12676.71 3.463739e-203 12682.15 7.097685e-203
## 73 TIM3 67 -6263.573 12661.15 8.311045e-200 12667.31 1.185926e-199
## 57 TIM1 67 -6263.631 12661.26 7.847574e-200 12667.43 1.119792e-199
## 77 TVMe 65 -6275.160 12680.32 5.706693e-204 12686.12 9.787040e-204
## 7 F81+G(4) 65 -6275.782 12681.56 3.061432e-204 12687.36 5.250389e-204
## 13 HKY 65 -6276.194 12682.39 2.027638e-204 12688.19 3.477420e-204
## 49 TPM3u 66 -6276.022 12684.04 8.867070e-205 12690.02 1.388146e-204
## 33 TPM1u 66 -6276.094 12684.19 8.243967e-205 12690.17 1.290599e-204
## 17 TrNe 63 -6296.975 12719.95 1.414288e-212 12725.39 2.898075e-212
## 69 TIM3e 64 -6296.937 12721.87 5.407528e-213 12727.49 1.014466e-212
## 53 TIM1e 64 -6296.938 12721.88 5.400399e-213 12727.49 1.013128e-212
## 9 K80 62 -6335.641 12795.28 6.202376e-229 12800.55 1.386198e-228
## 45 TPM3 63 -6335.582 12797.16 2.419369e-229 12802.61 4.957626e-229
## 25 TPM1 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 29 K81 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 2 JC+I 62 -6343.549 12811.10 2.280315e-232 12816.37 5.096384e-232
## 4 JC+G(4)+I 63 -6340.357 12806.71 2.043113e-231 12812.15 4.186625e-231
## 3 JC+G(4) 62 -6353.090 12830.18 1.639507e-236 12835.45 3.664211e-236
## 5 F81 64 -6638.961 13405.92 0.000000e+00 13411.54 0.000000e+00
## 1 JC 61 -6699.334 13520.67 0.000000e+00 13525.77 0.000000e+00
## BIC
## 68 12116.98
## 92 12124.04
## 44 12124.08
## 84 12132.04
## 66 12132.20
## 67 12132.98
## 43 12135.88
## 24 12136.27
## 76 12136.68
## 90 12138.14
## 16 12138.82
## 52 12139.86
## 42 12140.47
## 91 12141.91
## 60 12142.57
## 36 12145.11
## 83 12145.23
## 15 12146.57
## 82 12147.07
## 23 12147.45
## 51 12149.38
## 75 12150.15
## 74 12150.36
## 22 12150.74
## 50 12153.02
## 14 12153.19
## 35 12153.38
## 59 12154.21
## 58 12157.30
## 34 12159.65
## 64 12172.34
## 88 12178.53
## 62 12184.43
## 86 12189.93
## 63 12195.71
## 87 12204.04
## 72 12231.54
## 20 12232.41
## 56 12239.26
## 40 12240.01
## 70 12244.49
## 18 12245.76
## 80 12249.48
## 39 12249.86
## 19 12251.89
## 54 12252.91
## 71 12253.99
## 55 12258.93
## 79 12259.66
## 38 12270.57
## 78 12278.57
## 12 12291.82
## 48 12292.98
## 11 12297.77
## 28 12298.52
## 32 12298.52
## 47 12300.19
## 27 12304.83
## 31 12304.83
## 10 12314.43
## 46 12314.73
## 26 12321.38
## 30 12321.38
## 65 12936.83
## 61 12945.15
## 89 12951.00
## 41 12953.22
## 85 12959.63
## 81 12967.29
## 8 13011.48
## 21 13012.12
## 6 13012.63
## 37 13013.35
## 73 13019.16
## 57 13019.27
## 77 13027.64
## 7 13028.89
## 13 13029.71
## 49 13036.71
## 33 13036.85
## 17 13056.59
## 69 13063.85
## 53 13063.86
## 9 13126.57
## 45 13133.80
## 25 13133.84
## 29 13133.84
## 2 13142.39
## 4 13143.35
## 3 13161.47
## 5 13747.90
## 1 13846.62
Meilleur modele : TIM2+G(4)+I
env$`TIM2+G(4)+I`
## pml(tree = `tree_TIM2+G(4)+I`, data = data, bf = c(0.268171757414785,
## 0.270827799911465, 0.170916334661355, 0.290084108012395), Q = c(7.62145716626704,
## 50.5284652228583, 7.62145716626704, 1, 86.6493750028368, 1),
## model = "TIM2", inv = 0.588100254543259, k = 4, shape = 2.68433431260428)
#Matrice de distances par défaut (Jukes et Cantor)
dm <- dist.ml(mySequences_phangorn)
#Construction d'arbre par NJ
treeNJ <- NJ(dm)
#Calcul du score de maximum de vraisemblance
fit = pml(treeNJ, data=mySequences_phangorn)
#Phangorn nous permet de changer le modèle utilisé dans un objet
#On commence par intégrer les paramètres gamma et I (proportion de sites invariables)
fitTIM2 <- update(fit, k=4, inv=0.586110878594773, shape = 2.76728130721059)
#Recalcul des distances avec le modèle TIM2
fitTIM2 <- optim.pml(fitTIM2, model="TIM2", optInv=TRUE, optGamma=TRUE,optShape = TRUE, rearrangement = "stochastic", control = pml.control(trace = 0))
#Bootstrap
bs = bootstrap.pml(fitTIM2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE,control = pml.control(trace = 0))
#représentation graphique de l'arbre final
plotBS(midpoint(fitTIM2$tree), bs, p = 0, type="p", frame = "circle", cex = 0.6, bs.adj = c(0.5,0.5), bg = "white")
Conversion
#Cadre de lecture par default (NA)
mySequences_align_aa_ape = as.AAbin(mySequences_align_aa)
mySequences_phangorn_aa = as.phyDat.AAbin(mySequences_align_aa_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
#Cadre de lecture choisie : 1
mySequences_align_aa__cadre_1_ape = as.AAbin(mySequences_align_aa_cadre_1)
mySequences_phangorn_aa_cadre_1 = as.phyDat.AAbin(mySequences_align_aa__cadre_1_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
Matrice de distance
#Cadre de lecture par default (NA)
dist_LG <- dist.ml(mySequences_phangorn_aa, model = "LG")
dist_JTT <- dist.ml(mySequences_phangorn_aa, model = "JTT")
dist_Blosum62 <- dist.ml(mySequences_phangorn_aa, model = "Blosum62")
#Cadre de lecture choisie : 1
dist_LG_cadre1 <- dist.ml(mySequences_phangorn_aa_cadre_1, model = "LG")
dist_JTT_cadre1 <- dist.ml(mySequences_phangorn_aa_cadre_1, model = "JTT")
dist_Blosum62_cadre1 <- dist.ml(mySequences_phangorn_aa_cadre_1, model = "Blosum62")
Graphique de la matrice de distance
plot(dist_LG, main = "Valeurs de distance entre les séquences pour LG pour le cadre de lecture par defaut", ylab = "distance", xlab= "position")
plot(dist_JTT, main = "Valeurs de distance entre les séquences pour JTT pour le cadre de lecture par defaut", ylab = "distance", xlab= "position")
plot(dist_Blosum62, main = "Valeurs de distance entre les séquences pour Blosum62 pour le cadre de lecture par defaut", ylab = "distance", xlab= "position")
plot(dist_LG_cadre1, main = "Valeurs de distance entre les séquences pour LG pour le cadre de lecture 1", ylab = "distance", xlab= "position")
plot(dist_JTT_cadre1, main = "Valeurs de distance entre les séquences pour JTT pour le cadre de lecture 1", ylab = "distance", xlab= "position")
plot(dist_Blosum62_cadre1, main = "Valeurs de distance entre les séquences pour Blosum62 pour le cadre de lecture 1", ylab = "distance", xlab= "position")
Construction d’arbres avec le Neighbor-Joining
#Cadre de lecture par default (NA)
dist_LG_NJ <- NJ(dist_LG)
dist_JTT_NJ = NJ(dist_JTT)
dist_Blosum62_NJ = NJ(dist_Blosum62)
#Cadre de lecture choisie : 1
dist_LG_NJ_cadre1 = NJ(dist_LG_cadre1)
dist_JTT_NJ_cadre1 = NJ(dist_JTT_cadre1)
dist_Blosum62_NJ_cadre1 = NJ(dist_Blosum62_cadre1)
Rechercher le meilleur modèle pour le cadre par defaut
mySequences_modelTest_aa = phangorn::modelTest(mySequences_phangorn_aa, model = c("JTT","LG", "Blosum62"))
## Model df logLik AIC BIC
## JTT 61 -1790.436 3702.872 3961.171
## JTT+I 62 -1775.324 3674.647 3937.181
## JTT+G(4) 62 -1777.865 3679.731 3942.264
## JTT+G(4)+I 63 -1775.366 3676.731 3943.499
## LG 61 -1795.056 3712.113 3970.412
## LG+I 62 -1780.886 3685.771 3948.305
## LG+G(4) 62 -1782.945 3689.89 3952.424
## LG+G(4)+I 63 -1780.928 3687.856 3954.624
## Blosum62 61 -1789.301 3700.603 3958.902
## Blosum62+I 62 -1775.205 3674.411 3936.944
## Blosum62+G(4) 62 -1777.166 3678.332 3940.865
## Blosum62+G(4)+I 63 -1775.248 3676.496 3943.263
mySequences_modelTest_aa[order(mySequences_modelTest_aa$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 10 Blosum62+I 62 -1775.205 3674.411 3.609940e-01 3691.887 3.851836e-01
## 2 JTT+I 62 -1775.324 3674.647 3.206953e-01 3692.124 3.421846e-01
## 12 Blosum62+G(4)+I 63 -1775.248 3676.496 1.272802e-01 3694.576 1.003984e-01
## 4 JTT+G(4)+I 63 -1775.366 3676.731 1.131422e-01 3694.812 8.924639e-02
## 11 Blosum62+G(4) 62 -1777.166 3678.332 5.081598e-02 3695.808 5.422108e-02
## 3 JTT+G(4) 62 -1777.865 3679.731 2.524804e-02 3697.207 2.693987e-02
## 6 LG+I 62 -1780.886 3685.771 1.231861e-03 3703.248 1.314406e-03
## 8 LG+G(4)+I 63 -1780.928 3687.856 4.343156e-04 3705.937 3.425873e-04
## 7 LG+G(4) 62 -1782.945 3689.890 1.570951e-04 3707.367 1.676218e-04
## 9 Blosum62 61 -1789.301 3700.603 7.411858e-07 3717.487 1.063585e-06
## 1 JTT 61 -1790.436 3702.872 2.383650e-07 3719.756 3.420486e-07
## 5 LG 61 -1795.056 3712.113 2.347661e-09 3728.996 3.368842e-09
## BIC
## 10 3936.944
## 2 3937.181
## 12 3943.263
## 4 3943.499
## 11 3940.865
## 3 3942.264
## 6 3948.305
## 8 3954.624
## 7 3952.424
## 9 3958.902
## 1 3961.171
## 5 3970.412
mySequences_modelTest_aa[order(mySequences_modelTest_aa$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 10 Blosum62+I 62 -1775.205 3674.411 3.609940e-01 3691.887 3.851836e-01
## 2 JTT+I 62 -1775.324 3674.647 3.206953e-01 3692.124 3.421846e-01
## 11 Blosum62+G(4) 62 -1777.166 3678.332 5.081598e-02 3695.808 5.422108e-02
## 3 JTT+G(4) 62 -1777.865 3679.731 2.524804e-02 3697.207 2.693987e-02
## 12 Blosum62+G(4)+I 63 -1775.248 3676.496 1.272802e-01 3694.576 1.003984e-01
## 4 JTT+G(4)+I 63 -1775.366 3676.731 1.131422e-01 3694.812 8.924639e-02
## 6 LG+I 62 -1780.886 3685.771 1.231861e-03 3703.248 1.314406e-03
## 7 LG+G(4) 62 -1782.945 3689.890 1.570951e-04 3707.367 1.676218e-04
## 8 LG+G(4)+I 63 -1780.928 3687.856 4.343156e-04 3705.937 3.425873e-04
## 9 Blosum62 61 -1789.301 3700.603 7.411858e-07 3717.487 1.063585e-06
## 1 JTT 61 -1790.436 3702.872 2.383650e-07 3719.756 3.420486e-07
## 5 LG 61 -1795.056 3712.113 2.347661e-09 3728.996 3.368842e-09
## BIC
## 10 3936.944
## 2 3937.181
## 11 3940.865
## 3 3942.264
## 12 3943.263
## 4 3943.499
## 6 3948.305
## 7 3952.424
## 8 3954.624
## 9 3958.902
## 1 3961.171
## 5 3970.412
Meilleur modele: Blosum62+I
Rechercher le meilleur modèle pour le cadre 1
mySequences_modelTest_aa_cadre_1 = phangorn::modelTest(mySequences_phangorn_aa_cadre_1, model = c("JTT","LG", "Blosum62"))
## Model df logLik AIC BIC
## JTT 61 -2254.369 4630.738 4895.393
## JTT+I 62 -2251.546 4627.091 4896.084
## JTT+G(4) 62 -2250.274 4624.548 4893.54
## JTT+G(4)+I 63 -2250.274 4626.548 4899.879
## LG 61 -2254.105 4630.211 4894.865
## LG+I 62 -2251.311 4626.622 4895.615
## LG+G(4) 62 -2249.887 4623.775 4892.767
## LG+G(4)+I 63 -2249.856 4625.713 4899.044
## Blosum62 61 -2252.08 4626.16 4890.814
## Blosum62+I 62 -2251.753 4627.506 4896.499
## Blosum62+G(4) 62 -2250.298 4624.596 4893.589
## Blosum62+G(4)+I 63 -2250.283 4626.566 4899.898
mySequences_modelTest_aa_cadre_1[order(mySequences_modelTest_aa_cadre_1$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 7 LG+G(4) 62 -2249.887 4623.775 0.239235093 4639.305 0.244698908
## 3 JTT+G(4) 62 -2250.274 4624.548 0.162556819 4640.078 0.166269403
## 11 Blosum62+G(4) 62 -2250.298 4624.596 0.158638275 4640.127 0.162261364
## 8 LG+G(4)+I 63 -2249.856 4625.713 0.090783704 4641.776 0.071136220
## 9 Blosum62 61 -2252.080 4626.160 0.072595937 4641.168 0.096440867
## 4 JTT+G(4)+I 63 -2250.274 4626.548 0.059787012 4642.612 0.046847857
## 12 Blosum62+G(4)+I 63 -2250.283 4626.566 0.059246558 4642.630 0.046424369
## 6 LG+I 62 -2251.311 4626.622 0.057620910 4642.153 0.058936896
## 2 JTT+I 62 -2251.546 4627.091 0.045568358 4642.622 0.046609080
## 10 Blosum62+I 62 -2251.753 4627.506 0.037034140 4643.037 0.037879951
## 5 LG 61 -2254.105 4630.211 0.009576460 4645.219 0.012721953
## 1 JTT 61 -2254.369 4630.738 0.007356733 4645.746 0.009773132
## BIC
## 7 4892.767
## 3 4893.540
## 11 4893.589
## 8 4899.044
## 9 4890.814
## 4 4899.879
## 12 4899.898
## 6 4895.615
## 2 4896.084
## 10 4896.499
## 5 4894.865
## 1 4895.393
mySequences_modelTest_aa_cadre_1[order(mySequences_modelTest_aa_cadre_1$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 9 Blosum62 61 -2252.080 4626.160 0.072595937 4641.168 0.096440867
## 7 LG+G(4) 62 -2249.887 4623.775 0.239235093 4639.305 0.244698908
## 3 JTT+G(4) 62 -2250.274 4624.548 0.162556819 4640.078 0.166269403
## 11 Blosum62+G(4) 62 -2250.298 4624.596 0.158638275 4640.127 0.162261364
## 5 LG 61 -2254.105 4630.211 0.009576460 4645.219 0.012721953
## 1 JTT 61 -2254.369 4630.738 0.007356733 4645.746 0.009773132
## 6 LG+I 62 -2251.311 4626.622 0.057620910 4642.153 0.058936896
## 2 JTT+I 62 -2251.546 4627.091 0.045568358 4642.622 0.046609080
## 10 Blosum62+I 62 -2251.753 4627.506 0.037034140 4643.037 0.037879951
## 8 LG+G(4)+I 63 -2249.856 4625.713 0.090783704 4641.776 0.071136220
## 4 JTT+G(4)+I 63 -2250.274 4626.548 0.059787012 4642.612 0.046847857
## 12 Blosum62+G(4)+I 63 -2250.283 4626.566 0.059246558 4642.630 0.046424369
## BIC
## 9 4890.814
## 7 4892.767
## 3 4893.540
## 11 4893.589
## 5 4894.865
## 1 4895.393
## 6 4895.615
## 2 4896.084
## 10 4896.499
## 8 4899.044
## 4 4899.879
## 12 4899.898
Meilleur modele cadre 1 : LG+G(4)
Bootstrap avec 1000 iterations
#Cadre de lecture par default (NA)
dist_LG_NJ_boot <- bootstrap.phyDat(mySequences_phangorn_aa, FUN = function(x) NJ(dist.ml(x, model = "LG")), bs = 1000)
dist_JTT_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa, FUN = function(x) NJ(dist.ml(x, model = "JTT")), bs = 1000)
dist_Blosum62_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa, FUN = function(x) NJ(dist.ml(x, model = "Blosum62")), bs = 1000)
#Cadre de lecture choisie : 1
dist_cadre_1_LG_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa_cadre_1, FUN = function(x) NJ(dist.ml(x, model = "LG")), bs = 1000)
dist_cadre_1_JTT_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa_cadre_1, FUN = function(x) NJ(dist.ml(x, model = "JTT")), bs = 1000)
dist_cadre_1_Blosum62_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa_cadre_1, FUN = function(x) NJ(dist.ml(x, model = "Blosum62")), bs = 1000)
Générer un arbre consensuel à partir de l’ensemble d’arbres issus des itérations de bootstrap
p = 0.5 : une branche doit être “supportée” par au moins 50% des itérations pour être considérée dans l’arbre consensuel final.
#Cadre de lecture par default (NA)
cons_LG <- consensus(dist_LG_NJ_boot, p = 0.5)
cons_JTT <- consensus(dist_JTT_NJ_boot, p = 0.5)
cons_Blosum62 <- consensus(dist_Blosum62_NJ_boot, p = 0.5)
#Cadre de lecture choisie : 1
cons_cadre_1_LG <- consensus(dist_cadre_1_LG_NJ_boot, p = 0.5)
cons_cadre_1_JTT <- consensus(dist_cadre_1_JTT_NJ_boot, p = 0.5)
cons_cadre_1_Blosum62 <- consensus(dist_cadre_1_Blosum62_NJ_boot, p = 0.5)
Comparaison des bootstraps
bootstrap_comparisons <- round(cor(cbind(cons_LG$node.label,cons_JTT$node.label,cons_Blosum62$node.label, cons_cadre_1_LG$node.label,cons_cadre_1_JTT$node.label,cons_cadre_1_Blosum62$node.label )),3)
## Warning in cbind(...): number of rows of result is not a multiple of vector
## length (arg 5)
# Ajouter les noms aux colonnes et aux lignes
colnames(bootstrap_comparisons) <- c("LG", "JTT", "Blosum62", "LG_cadre1", "JTT_cadre1", "Blosum62_cadre1")
rownames(bootstrap_comparisons) <- c("LG", "JTT", "Blosum62", "LG_cadre1", "JTT_cadre1", "Blosum62_cadre1")
bootstrap_comparisons
## LG JTT Blosum62 LG_cadre1 JTT_cadre1 Blosum62_cadre1
## LG 1.000 0.986 0.978 0.599 0.337 0.177
## JTT 0.986 1.000 0.982 0.594 0.362 0.158
## Blosum62 0.978 0.982 1.000 0.473 0.269 0.197
## LG_cadre1 0.599 0.594 0.473 1.000 0.363 -0.009
## JTT_cadre1 0.337 0.362 0.269 0.363 1.000 0.048
## Blosum62_cadre1 0.177 0.158 0.197 -0.009 0.048 1.000
Visualisation des bootstraps
plot(cons_LG, main = "LG, cadre par defaut", no.margin = TRUE)
nodelabels(cons_LG$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
plot(cons_JTT,, main = "JTT, cadre par defaut", no.margin = TRUE)
nodelabels(cons_JTT$node.label * 100, bg = "white", frame = "circle", cex = 0.6)
plot(cons_Blosum62, main = "Blosum62, cadre par defaut", no.margin = TRUE)
nodelabels(cons_Blosum62$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
plot(cons_cadre_1_LG, main = "LG, cadre 1", no.margin = TRUE)
nodelabels(cons_cadre_1_LG$node.label * 100,
bg ="white",
frame = "circle", cex = 0.6)
plot(cons_cadre_1_JTT, main = "JTT, cadre 1", no.margin = TRUE)
nodelabels(cons_cadre_1_JTT$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
plot(cons_cadre_1_Blosum62,main = "Blosum62, cadre 1", no.margin = TRUE)
nodelabels(cons_cadre_1_Blosum62$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
Alignements
# Cadre 1
Align_aa_cadre1 = AlignTranslation(mySequences,
sense = "+",
readingFrame = 1,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.06 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.06 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
# Cadre 2
Align_aa_cadre2 = AlignTranslation(mySequences,
sense = "+",
readingFrame = 2,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 0.03 secs
# Cadre 3
Align_aa_cadre3 = AlignTranslation(mySequences,
sense = "+",
readingFrame = 3,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.1 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.07 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 0.02 secs
Conversions
# Cadre 1
Align_aa_cadre1_ape = as.AAbin(Align_aa_cadre1)
Align_aa_cadre1_phangorn = as.phyDat.AAbin(Align_aa_cadre1_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
# Cadre 2
Align_aa_cadre2_ape = as.AAbin(Align_aa_cadre2)
Align_aa_cadre2_phangorn = as.phyDat.AAbin(Align_aa_cadre2_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
# Cadre 3
Align_aa_cadre3_ape = as.AAbin(Align_aa_cadre3)
Align_aa_cadre3_phangorn = as.phyDat.AAbin(Align_aa_cadre3_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
# Cadre 1
modelTest_aa_cadre1 = phangorn::modelTest(Align_aa_cadre1_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 61 -2263.381 4648.762 4913.416
## WAG+I 62 -2261.887 4647.774 4916.767
## WAG+G(4) 62 -2260.337 4644.675 4913.668
## WAG+G(4)+I 63 -2260.298 4646.597 4919.928
## JTT 61 -2260.149 4642.297 4906.951
## JTT+I 62 -2257.322 4638.645 4907.637
## JTT+G(4) 62 -2255.785 4635.57 4904.563
## JTT+G(4)+I 63 -2255.785 4637.571 4910.902
## LG 61 -2259.409 4640.818 4905.472
## LG+I 62 -2256.612 4637.223 4906.216
## LG+G(4) 62 -2254.886 4633.773 4902.766
## LG+G(4)+I 63 -2254.857 4635.714 4909.045
## Dayhoff 61 -2344.747 4811.493 5076.147
## Dayhoff+I 62 -2286.289 4696.578 4965.571
## Dayhoff+G(4) 62 -2347.623 4819.246 5088.239
## Dayhoff+G(4)+I 63 -2351.927 4829.853 5103.185
## cpREV 61 -2244.43 4610.86 4875.514
## cpREV+I 62 -2243.668 4611.336 4880.328
## cpREV+G(4) 62 -2241.094 4606.189 4875.181
## cpREV+G(4)+I 63 -2241.053 4608.105 4881.437
## mtmam 61 -2305.294 4732.587 4997.242
## mtmam+I 62 -2302.664 4729.329 4998.321
## mtmam+G(4) 62 -2304.277 4732.554 5001.547
## mtmam+G(4)+I 63 -2302.695 4731.389 5004.721
## mtArt 61 -2197.083 4516.167 4780.821
## mtArt+I 62 -2194.926 4513.851 4782.844
## mtArt+G(4) 62 -2192.365 4508.731 4777.724
## mtArt+G(4)+I 63 -2192.204 4510.408 4783.739
## MtZoa 61 -2184.753 4491.506 4756.161
## MtZoa+I 62 -2183.359 4490.717 4759.71
## MtZoa+G(4) 62 -2181.142 4486.283 4755.276
## MtZoa+G(4)+I 63 -2181.117 4488.233 4761.565
## mtREV24 61 -2200.49 4522.979 4787.634
## mtREV24+I 62 -2198.709 4521.418 4790.41
## mtREV24+G(4) 62 -2194.307 4512.613 4781.606
## mtREV24+G(4)+I 63 -2194.307 4514.613 4787.945
## VT 61 -2254.936 4631.871 4896.525
## VT+I 62 -2253.329 4630.659 4899.651
## VT+G(4) 62 -2249.596 4623.192 4892.184
## VT+G(4)+I 63 -2249.596 4625.192 4898.524
## RtREV 61 -2270.525 4663.05 4927.704
## RtREV+I 62 -2268.845 4661.69 4930.683
## RtREV+G(4) 62 -2266.996 4657.991 4926.984
## RtREV+G(4)+I 63 -2266.991 4659.982 4933.314
## HIVw 61 -2352.958 4827.917 5092.571
## HIVw+I 62 -2343.931 4811.862 5080.855
## HIVw+G(4) 62 -2339.832 4803.664 5072.657
## HIVw+G(4)+I 63 -2339.787 4805.574 5078.906
## HIVb 61 -2288.961 4699.921 4964.575
## HIVb+I 62 -2284.819 4693.638 4962.631
## HIVb+G(4) 62 -2283.384 4690.768 4959.761
## HIVb+G(4)+I 63 -2283.457 4692.914 4966.246
## FLU 61 -2288.97 4699.94 4964.594
## FLU+I 62 -2285.155 4694.311 4963.304
## FLU+G(4) 62 -2285.704 4695.408 4964.401
## FLU+G(4)+I 63 -2284.923 4695.846 4969.177
## Blosum62 61 -2257.9 4637.8 4902.454
## Blosum62+I 62 -2257.572 4639.144 4908.136
## Blosum62+G(4) 62 -2255.824 4635.648 4904.641
## Blosum62+G(4)+I 63 -2255.807 4637.614 4910.946
## Dayhoff_DCMut 61 -2344.547 4811.094 5075.748
## Dayhoff_DCMut+I 62 -2347.441 4818.882 5087.875
## Dayhoff_DCMut+G(4) 62 -2347.422 4818.845 5087.837
## Dayhoff_DCMut+G(4)+I 63 -2347.55 4821.101 5094.432
## JTT_DCMut 61 -2260.683 4643.365 4908.02
## JTT_DCMut+I 62 -2257.895 4639.791 4908.784
## JTT_DCMut+G(4) 62 -2256.351 4636.702 4905.695
## JTT_DCMut+G(4)+I 63 -2256.351 4638.702 4912.034
# Cadre 2
modelTest_aa_cadre2 = phangorn::modelTest(Align_aa_cadre2_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 61 -5573.273 11268.55 11532.44
## WAG+I 62 -5571.499 11267 11535.22
## WAG+G(4) 62 -5565.296 11254.59 11522.81
## WAG+G(4)+I 63 -5565.296 11256.59 11529.14
## JTT 61 -5272.829 10667.66 10931.55
## JTT+I 62 -5271.67 10667.34 10935.56
## JTT+G(4) 62 -5270.491 10664.98 10933.2
## JTT+G(4)+I 63 -5270.338 10666.68 10939.22
## LG 61 -5734.226 11590.45 11854.35
## LG+I 62 -5732.276 11588.55 11856.77
## LG+G(4) 62 -5722.814 11569.63 11837.85
## LG+G(4)+I 63 -5722.815 11571.63 11844.18
## Dayhoff 61 -5666.569 11455.14 11719.03
## Dayhoff+I 62 -5661.948 11447.9 11716.12
## Dayhoff+G(4) 62 -5654.7 11433.4 11701.62
## Dayhoff+G(4)+I 63 -5654.509 11435.02 11707.57
## cpREV 61 -5518.954 11159.91 11423.8
## cpREV+I 62 -5515.34 11154.68 11422.9
## cpREV+G(4) 62 -5505.296 11134.59 11402.81
## cpREV+G(4)+I 63 -5505.264 11136.53 11409.07
## mtmam 61 -5520.483 11162.97 11426.86
## mtmam+I 62 -5520.063 11164.13 11432.35
## mtmam+G(4) 62 -5504.986 11133.97 11402.19
## mtmam+G(4)+I 63 -5504.987 11135.97 11408.52
## mtArt 61 -5988.27 12098.54 12362.44
## mtArt+I 62 -5976.513 12077.03 12345.25
## mtArt+G(4) 62 -5878.724 11881.45 12149.67
## mtArt+G(4)+I 63 -5878.727 11883.45 12156
## MtZoa 61 -5839.378 11800.76 12064.65
## MtZoa+I 62 -5832.736 11789.47 12057.69
## MtZoa+G(4) 62 -5780.309 11684.62 11952.84
## MtZoa+G(4)+I 63 -5780.31 11686.62 11959.17
## mtREV24 61 -5477.613 11077.23 11341.12
## mtREV24+I 62 -5476.042 11076.08 11344.31
## mtREV24+G(4) 62 -5453.626 11031.25 11299.47
## mtREV24+G(4)+I 63 -5453.627 11033.25 11305.8
## VT 61 -5715.503 11553.01 11816.9
## VT+I 62 -5713.168 11550.34 11818.56
## VT+G(4) 62 -5701.884 11527.77 11795.99
## VT+G(4)+I 63 -5701.862 11529.72 11802.27
## RtREV 61 -5773.701 11669.4 11933.3
## RtREV+I 62 -5770.184 11664.37 11932.59
## RtREV+G(4) 62 -5757.388 11638.78 11907
## RtREV+G(4)+I 63 -5757.38 11640.76 11913.31
## HIVw 61 -5105.614 10333.23 10597.12
## HIVw+I 62 -5101.986 10327.97 10596.19
## HIVw+G(4) 62 -5102.354 10328.71 10596.93
## HIVw+G(4)+I 63 -5100.988 10327.98 10600.52
## HIVb 61 -5237.43 10596.86 10860.75
## HIVb+I 62 -5235.771 10595.54 10863.76
## HIVb+G(4) 62 -5231.911 10587.82 10856.04
## HIVb+G(4)+I 63 -5231.855 10589.71 10862.26
## FLU 61 -5329.737 10781.47 11045.37
## FLU+I 62 -5328.047 10780.09 11048.31
## FLU+G(4) 62 -5323.252 10770.5 11038.72
## FLU+G(4)+I 63 -5323.22 10772.44 11044.99
## Blosum62 61 -5725.452 11572.9 11836.8
## Blosum62+I 62 -5724.758 11573.52 11841.74
## Blosum62+G(4) 62 -5717.55 11559.1 11827.32
## Blosum62+G(4)+I 63 -5717.552 11561.1 11833.65
## Dayhoff_DCMut 61 -5666.022 11454.04 11717.94
## Dayhoff_DCMut+I 62 -5661.455 11446.91 11715.13
## Dayhoff_DCMut+G(4) 62 -5654.327 11432.65 11700.88
## Dayhoff_DCMut+G(4)+I 63 -5654.134 11434.27 11706.82
## JTT_DCMut 61 -5272.287 10666.57 10930.47
## JTT_DCMut+I 62 -5271.007 10666.01 10934.23
## JTT_DCMut+G(4) 62 -5269.726 10663.45 10931.67
## JTT_DCMut+G(4)+I 63 -5269.558 10665.12 10937.66
# Cadre 3
modelTest_aa_cadre3 = phangorn::modelTest(Align_aa_cadre3_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 61 -5555.198 11232.4 11493.39
## WAG+I 62 -5551.78 11227.56 11492.83
## WAG+G(4) 62 -5541.009 11206.02 11471.29
## WAG+G(4)+I 63 -5541.007 11208.01 11477.56
## JTT 61 -5360.294 10842.59 11103.58
## JTT+I 62 -5357.455 10838.91 11104.18
## JTT+G(4) 62 -5348.833 10821.67 11086.93
## JTT+G(4)+I 63 -5348.822 10823.64 11093.19
## LG 61 -5614.854 11351.71 11612.7
## LG+I 62 -5610.756 11345.51 11610.78
## LG+G(4) 62 -5596.215 11316.43 11581.7
## LG+G(4)+I 63 -5596.215 11318.43 11587.98
## Dayhoff 61 -5642.067 11406.13 11667.12
## Dayhoff+I 62 -5638.096 11400.19 11665.46
## Dayhoff+G(4) 62 -5620.341 11364.68 11629.95
## Dayhoff+G(4)+I 63 -5620.411 11366.82 11636.37
## cpREV 61 -5477.362 11076.72 11337.71
## cpREV+I 62 -5470.87 11065.74 11331.01
## cpREV+G(4) 62 -5448.791 11021.58 11286.85
## cpREV+G(4)+I 63 -5448.787 11023.57 11293.12
## mtmam 61 -5378.721 10879.44 11140.43
## mtmam+I 62 -5377.876 10879.75 11145.02
## mtmam+G(4) 62 -5348.536 10821.07 11086.34
## mtmam+G(4)+I 63 -5348.536 10823.07 11092.62
## mtArt 61 -5837.166 11796.33 12057.32
## mtArt+I 62 -5825.196 11774.39 12039.66
## mtArt+G(4) 62 -5735.987 11595.97 11861.24
## mtArt+G(4)+I 63 -5735.988 11597.98 11867.52
## MtZoa 61 -5631.963 11385.93 11646.92
## MtZoa+I 62 -5623.709 11371.42 11636.69
## MtZoa+G(4) 62 -5563.323 11250.65 11515.91
## MtZoa+G(4)+I 63 -5563.324 11252.65 11522.2
## mtREV24 61 -5482.664 11087.33 11348.32
## mtREV24+I 62 -5475.823 11075.65 11340.91
## mtREV24+G(4) 62 -5437.664 10999.33 11264.6
## mtREV24+G(4)+I 63 -5437.664 11001.33 11270.88
## VT 61 -5856.713 11835.43 12096.42
## VT+I 62 -5844.255 11812.51 12077.78
## VT+G(4) 62 -5802.941 11729.88 11995.15
## VT+G(4)+I 63 -5802.941 11731.88 12001.43
## RtREV 61 -5758.647 11639.29 11900.28
## RtREV+I 62 -5754.169 11632.34 11897.61
## RtREV+G(4) 62 -5739.59 11603.18 11868.45
## RtREV+G(4)+I 63 -5739.561 11605.12 11874.67
## HIVw 61 -5296.14 10714.28 10975.27
## HIVw+I 62 -5289.262 10702.52 10967.79
## HIVw+G(4) 62 -5274.747 10673.49 10938.76
## HIVw+G(4)+I 63 -5274.432 10674.86 10944.41
## HIVb 61 -5408.02 10938.04 11199.03
## HIVb+I 62 -5403.549 10931.1 11196.37
## HIVb+G(4) 62 -5386.722 10897.44 11162.71
## HIVb+G(4)+I 63 -5386.72 10899.44 11168.99
## FLU 61 -5404.973 10931.95 11192.93
## FLU+I 62 -5398.516 10921.03 11186.3
## FLU+G(4) 62 -5372.332 10868.66 11133.93
## FLU+G(4)+I 63 -5372.299 10870.6 11140.14
## Blosum62 61 -5729.07 11580.14 11841.13
## Blosum62+I 62 -5725.072 11574.14 11839.41
## Blosum62+G(4) 62 -5715.334 11554.67 11819.94
## Blosum62+G(4)+I 63 -5715.306 11556.61 11826.16
## Dayhoff_DCMut 61 -5641.668 11405.34 11666.33
## Dayhoff_DCMut+I 62 -5637.732 11399.46 11664.73
## Dayhoff_DCMut+G(4) 62 -5620.165 11364.33 11629.6
## Dayhoff_DCMut+G(4)+I 63 -5620.234 11366.47 11636.02
## JTT_DCMut 61 -5369.642 10861.28 11122.27
## JTT_DCMut+I 62 -5366.753 10857.51 11122.77
## JTT_DCMut+G(4) 62 -5357.833 10839.67 11104.93
## JTT_DCMut+G(4)+I 63 -5357.824 10841.65 11111.19
Trouver le meilleur modele
# Cadre 1
env <- attr(modelTest_aa_cadre1, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
modelTest_aa_cadre1[order(modelTest_aa_cadre1$AIC), ]
## Model df logLik AIC AICw AICc
## 31 MtZoa+G(4) 62 -2181.142 4486.283 6.412018e-01 4501.814
## 32 MtZoa+G(4)+I 63 -2181.117 4488.233 2.418431e-01 4504.297
## 30 MtZoa+I 62 -2183.359 4490.717 6.985883e-02 4506.248
## 29 MtZoa 61 -2184.753 4491.506 4.708150e-02 4506.514
## 27 mtArt+G(4) 62 -2192.365 4508.731 8.563006e-06 4524.261
## 28 mtArt+G(4)+I 63 -2192.204 4510.408 3.701626e-06 4526.472
## 35 mtREV24+G(4) 62 -2194.307 4512.613 1.229028e-06 4528.144
## 26 mtArt+I 62 -2194.926 4513.851 6.617641e-07 4529.382
## 36 mtREV24+G(4)+I 63 -2194.307 4514.613 4.520787e-07 4530.677
## 25 mtArt 61 -2197.083 4516.167 2.079078e-07 4531.175
## 34 mtREV24+I 62 -2198.709 4521.418 1.505530e-08 4536.948
## 33 mtREV24 61 -2200.490 4522.979 6.895727e-09 4537.987
## 19 cpREV+G(4) 62 -2241.094 4606.189 5.887188e-27 4621.719
## 20 cpREV+G(4)+I 63 -2241.053 4608.105 2.257869e-27 4624.169
## 17 cpREV 61 -2244.430 4610.860 5.696190e-28 4625.868
## 18 cpREV+I 62 -2243.668 4611.336 4.489985e-28 4626.866
## 39 VT+G(4) 62 -2249.596 4623.192 1.196018e-30 4638.722
## 40 VT+G(4)+I 63 -2249.596 4625.192 4.398502e-31 4641.256
## 38 VT+I 62 -2253.329 4630.659 2.859660e-32 4646.189
## 37 VT 61 -2254.936 4631.871 1.559521e-32 4646.879
## 11 LG+G(4) 62 -2254.886 4633.773 6.026988e-33 4649.303
## 7 JTT+G(4) 62 -2255.785 4635.570 2.453398e-33 4651.101
## 59 Blosum62+G(4) 62 -2255.824 4635.648 2.360112e-33 4651.179
## 12 LG+G(4)+I 63 -2254.857 4635.714 2.283664e-33 4651.777
## 67 JTT_DCMut+G(4) 62 -2256.351 4636.702 1.393216e-33 4652.233
## 10 LG+I 62 -2256.612 4637.223 1.073514e-33 4652.754
## 8 JTT+G(4)+I 63 -2255.785 4637.571 9.023447e-34 4653.634
## 60 Blosum62+G(4)+I 63 -2255.807 4637.614 8.828675e-34 4653.678
## 57 Blosum62 61 -2257.900 4637.800 8.045825e-34 4652.808
## 6 JTT+I 62 -2257.322 4638.645 5.274485e-34 4654.175
## 68 JTT_DCMut+G(4)+I 63 -2256.351 4638.702 5.124147e-34 4654.766
## 58 Blosum62+I 62 -2257.572 4639.144 4.109857e-34 4654.674
## 66 JTT_DCMut+I 62 -2257.895 4639.791 2.973330e-34 4655.322
## 9 LG 61 -2259.409 4640.818 1.779159e-34 4655.826
## 5 JTT 61 -2260.149 4642.297 8.492553e-35 4657.305
## 65 JTT_DCMut 61 -2260.683 4643.365 4.978408e-35 4658.373
## 3 WAG+G(4) 62 -2260.337 4644.675 2.586405e-35 4660.206
## 4 WAG+G(4)+I 63 -2260.298 4646.597 9.894474e-36 4662.660
## 2 WAG+I 62 -2261.887 4647.774 5.491625e-36 4663.305
## 1 WAG 61 -2263.381 4648.762 3.351107e-36 4663.770
## 43 RtREV+G(4) 62 -2266.996 4657.991 3.319483e-38 4673.522
## 44 RtREV+G(4)+I 63 -2266.991 4659.982 1.226873e-38 4676.046
## 42 RtREV+I 62 -2268.845 4661.690 5.223955e-39 4677.220
## 41 RtREV 61 -2270.525 4663.050 2.646470e-39 4678.058
## 51 HIVb+G(4) 62 -2283.384 4690.768 2.533149e-45 4706.299
## 52 HIVb+G(4)+I 63 -2283.457 4692.914 8.662389e-46 4708.978
## 50 HIVb+I 62 -2284.819 4693.638 6.031978e-46 4709.169
## 54 FLU+I 62 -2285.155 4694.311 4.309048e-46 4709.842
## 55 FLU+G(4) 62 -2285.704 4695.408 2.489500e-46 4710.939
## 56 FLU+G(4)+I 63 -2284.923 4695.846 2.000513e-46 4711.909
## 14 Dayhoff+I 62 -2286.289 4696.578 1.387176e-46 4712.109
## 49 HIVb 61 -2288.961 4699.921 2.607059e-47 4714.929
## 53 FLU 61 -2288.970 4699.940 2.582352e-47 4714.948
## 22 mtmam+I 62 -2302.664 4729.329 1.072519e-53 4744.859
## 24 mtmam+G(4)+I 63 -2302.695 4731.389 3.827892e-54 4747.453
## 23 mtmam+G(4) 62 -2304.277 4732.554 2.137519e-54 4748.085
## 21 mtmam 61 -2305.294 4732.587 2.102600e-54 4747.595
## 47 HIVw+G(4) 62 -2339.832 4803.664 7.738658e-70 4819.195
## 48 HIVw+G(4)+I 63 -2339.787 4805.574 2.977609e-70 4821.638
## 61 Dayhoff_DCMut 61 -2344.547 4811.094 1.884843e-71 4826.102
## 13 Dayhoff 61 -2344.747 4811.493 1.543860e-71 4826.501
## 46 HIVw+I 62 -2343.931 4811.862 1.283894e-71 4827.393
## 63 Dayhoff_DCMut+G(4) 62 -2347.422 4818.845 3.910641e-73 4834.375
## 62 Dayhoff_DCMut+I 62 -2347.441 4818.882 3.838174e-73 4834.413
## 15 Dayhoff+G(4) 62 -2347.623 4819.246 3.199604e-73 4834.777
## 64 Dayhoff_DCMut+G(4)+I 63 -2347.550 4821.101 1.265703e-73 4837.164
## 45 HIVw 61 -2352.958 4827.917 4.190232e-75 4842.925
## 16 Dayhoff+G(4)+I 63 -2351.927 4829.853 1.591242e-75 4845.917
## AICcw BIC
## 31 6.696654e-01 4755.276
## 32 1.934962e-01 4761.565
## 30 7.295994e-02 4759.710
## 29 6.386385e-02 4756.161
## 27 8.943127e-06 4777.724
## 28 2.961634e-06 4783.739
## 35 1.283586e-06 4781.606
## 26 6.911406e-07 4782.844
## 36 3.617037e-07 4787.945
## 25 2.820172e-07 4780.821
## 34 1.572362e-08 4790.410
## 33 9.353731e-09 4787.634
## 19 6.148527e-27 4875.181
## 20 1.806498e-27 4881.437
## 17 7.726615e-28 4875.514
## 18 4.689300e-28 4880.328
## 39 1.249111e-30 4892.184
## 40 3.519198e-31 4898.524
## 38 2.986603e-32 4899.651
## 37 2.115418e-32 4896.525
## 11 6.294533e-33 4902.766
## 7 2.562307e-33 4904.563
## 59 2.464880e-33 4904.641
## 12 1.827137e-33 4909.045
## 67 1.455063e-33 4905.695
## 10 1.121168e-33 4906.216
## 8 7.219571e-34 4910.902
## 60 7.063736e-34 4910.946
## 57 1.091378e-33 4902.454
## 6 5.508625e-34 4907.637
## 68 4.099779e-34 4912.034
## 58 4.292298e-34 4908.136
## 66 3.105320e-34 4908.784
## 9 2.413346e-34 4905.472
## 5 1.151975e-34 4906.951
## 65 6.752978e-35 4908.020
## 3 2.701218e-35 4913.668
## 4 7.916471e-36 4919.928
## 2 5.735404e-36 4916.767
## 1 4.545620e-36 4913.416
## 43 3.466838e-38 4926.984
## 44 9.816090e-39 4933.314
## 42 5.455852e-39 4930.683
## 41 3.589813e-39 4927.704
## 51 2.645598e-45 4959.761
## 52 6.930691e-46 4966.246
## 50 6.299744e-46 4962.631
## 54 4.500331e-46 4963.304
## 55 2.600012e-46 4964.401
## 56 1.600591e-46 4969.177
## 14 1.448754e-46 4965.571
## 49 3.536354e-47 4964.575
## 53 3.502839e-47 4964.594
## 22 1.120130e-53 4998.321
## 24 3.062659e-54 5004.721
## 23 2.232406e-54 5001.547
## 21 2.852079e-54 4997.242
## 47 8.082185e-70 5072.657
## 48 2.382355e-70 5078.906
## 61 2.556701e-71 5075.748
## 13 2.094174e-71 5076.147
## 46 1.340888e-71 5080.855
## 63 4.084238e-73 5087.837
## 62 4.008554e-73 5087.875
## 15 3.341638e-73 5088.239
## 64 1.012676e-73 5094.432
## 45 5.683853e-75 5092.571
## 16 1.273137e-75 5103.185
modelTest_aa_cadre1[order(modelTest_aa_cadre1$BIC), ]
## Model df logLik AIC AICw AICc
## 31 MtZoa+G(4) 62 -2181.142 4486.283 6.412018e-01 4501.814
## 29 MtZoa 61 -2184.753 4491.506 4.708150e-02 4506.514
## 30 MtZoa+I 62 -2183.359 4490.717 6.985883e-02 4506.248
## 32 MtZoa+G(4)+I 63 -2181.117 4488.233 2.418431e-01 4504.297
## 27 mtArt+G(4) 62 -2192.365 4508.731 8.563006e-06 4524.261
## 25 mtArt 61 -2197.083 4516.167 2.079078e-07 4531.175
## 35 mtREV24+G(4) 62 -2194.307 4512.613 1.229028e-06 4528.144
## 26 mtArt+I 62 -2194.926 4513.851 6.617641e-07 4529.382
## 28 mtArt+G(4)+I 63 -2192.204 4510.408 3.701626e-06 4526.472
## 33 mtREV24 61 -2200.490 4522.979 6.895727e-09 4537.987
## 36 mtREV24+G(4)+I 63 -2194.307 4514.613 4.520787e-07 4530.677
## 34 mtREV24+I 62 -2198.709 4521.418 1.505530e-08 4536.948
## 19 cpREV+G(4) 62 -2241.094 4606.189 5.887188e-27 4621.719
## 17 cpREV 61 -2244.430 4610.860 5.696190e-28 4625.868
## 18 cpREV+I 62 -2243.668 4611.336 4.489985e-28 4626.866
## 20 cpREV+G(4)+I 63 -2241.053 4608.105 2.257869e-27 4624.169
## 39 VT+G(4) 62 -2249.596 4623.192 1.196018e-30 4638.722
## 37 VT 61 -2254.936 4631.871 1.559521e-32 4646.879
## 40 VT+G(4)+I 63 -2249.596 4625.192 4.398502e-31 4641.256
## 38 VT+I 62 -2253.329 4630.659 2.859660e-32 4646.189
## 57 Blosum62 61 -2257.900 4637.800 8.045825e-34 4652.808
## 11 LG+G(4) 62 -2254.886 4633.773 6.026988e-33 4649.303
## 7 JTT+G(4) 62 -2255.785 4635.570 2.453398e-33 4651.101
## 59 Blosum62+G(4) 62 -2255.824 4635.648 2.360112e-33 4651.179
## 9 LG 61 -2259.409 4640.818 1.779159e-34 4655.826
## 67 JTT_DCMut+G(4) 62 -2256.351 4636.702 1.393216e-33 4652.233
## 10 LG+I 62 -2256.612 4637.223 1.073514e-33 4652.754
## 5 JTT 61 -2260.149 4642.297 8.492553e-35 4657.305
## 6 JTT+I 62 -2257.322 4638.645 5.274485e-34 4654.175
## 65 JTT_DCMut 61 -2260.683 4643.365 4.978408e-35 4658.373
## 58 Blosum62+I 62 -2257.572 4639.144 4.109857e-34 4654.674
## 66 JTT_DCMut+I 62 -2257.895 4639.791 2.973330e-34 4655.322
## 12 LG+G(4)+I 63 -2254.857 4635.714 2.283664e-33 4651.777
## 8 JTT+G(4)+I 63 -2255.785 4637.571 9.023447e-34 4653.634
## 60 Blosum62+G(4)+I 63 -2255.807 4637.614 8.828675e-34 4653.678
## 68 JTT_DCMut+G(4)+I 63 -2256.351 4638.702 5.124147e-34 4654.766
## 1 WAG 61 -2263.381 4648.762 3.351107e-36 4663.770
## 3 WAG+G(4) 62 -2260.337 4644.675 2.586405e-35 4660.206
## 2 WAG+I 62 -2261.887 4647.774 5.491625e-36 4663.305
## 4 WAG+G(4)+I 63 -2260.298 4646.597 9.894474e-36 4662.660
## 43 RtREV+G(4) 62 -2266.996 4657.991 3.319483e-38 4673.522
## 41 RtREV 61 -2270.525 4663.050 2.646470e-39 4678.058
## 42 RtREV+I 62 -2268.845 4661.690 5.223955e-39 4677.220
## 44 RtREV+G(4)+I 63 -2266.991 4659.982 1.226873e-38 4676.046
## 51 HIVb+G(4) 62 -2283.384 4690.768 2.533149e-45 4706.299
## 50 HIVb+I 62 -2284.819 4693.638 6.031978e-46 4709.169
## 54 FLU+I 62 -2285.155 4694.311 4.309048e-46 4709.842
## 55 FLU+G(4) 62 -2285.704 4695.408 2.489500e-46 4710.939
## 49 HIVb 61 -2288.961 4699.921 2.607059e-47 4714.929
## 53 FLU 61 -2288.970 4699.940 2.582352e-47 4714.948
## 14 Dayhoff+I 62 -2286.289 4696.578 1.387176e-46 4712.109
## 52 HIVb+G(4)+I 63 -2283.457 4692.914 8.662389e-46 4708.978
## 56 FLU+G(4)+I 63 -2284.923 4695.846 2.000513e-46 4711.909
## 21 mtmam 61 -2305.294 4732.587 2.102600e-54 4747.595
## 22 mtmam+I 62 -2302.664 4729.329 1.072519e-53 4744.859
## 23 mtmam+G(4) 62 -2304.277 4732.554 2.137519e-54 4748.085
## 24 mtmam+G(4)+I 63 -2302.695 4731.389 3.827892e-54 4747.453
## 47 HIVw+G(4) 62 -2339.832 4803.664 7.738658e-70 4819.195
## 61 Dayhoff_DCMut 61 -2344.547 4811.094 1.884843e-71 4826.102
## 13 Dayhoff 61 -2344.747 4811.493 1.543860e-71 4826.501
## 48 HIVw+G(4)+I 63 -2339.787 4805.574 2.977609e-70 4821.638
## 46 HIVw+I 62 -2343.931 4811.862 1.283894e-71 4827.393
## 63 Dayhoff_DCMut+G(4) 62 -2347.422 4818.845 3.910641e-73 4834.375
## 62 Dayhoff_DCMut+I 62 -2347.441 4818.882 3.838174e-73 4834.413
## 15 Dayhoff+G(4) 62 -2347.623 4819.246 3.199604e-73 4834.777
## 45 HIVw 61 -2352.958 4827.917 4.190232e-75 4842.925
## 64 Dayhoff_DCMut+G(4)+I 63 -2347.550 4821.101 1.265703e-73 4837.164
## 16 Dayhoff+G(4)+I 63 -2351.927 4829.853 1.591242e-75 4845.917
## AICcw BIC
## 31 6.696654e-01 4755.276
## 29 6.386385e-02 4756.161
## 30 7.295994e-02 4759.710
## 32 1.934962e-01 4761.565
## 27 8.943127e-06 4777.724
## 25 2.820172e-07 4780.821
## 35 1.283586e-06 4781.606
## 26 6.911406e-07 4782.844
## 28 2.961634e-06 4783.739
## 33 9.353731e-09 4787.634
## 36 3.617037e-07 4787.945
## 34 1.572362e-08 4790.410
## 19 6.148527e-27 4875.181
## 17 7.726615e-28 4875.514
## 18 4.689300e-28 4880.328
## 20 1.806498e-27 4881.437
## 39 1.249111e-30 4892.184
## 37 2.115418e-32 4896.525
## 40 3.519198e-31 4898.524
## 38 2.986603e-32 4899.651
## 57 1.091378e-33 4902.454
## 11 6.294533e-33 4902.766
## 7 2.562307e-33 4904.563
## 59 2.464880e-33 4904.641
## 9 2.413346e-34 4905.472
## 67 1.455063e-33 4905.695
## 10 1.121168e-33 4906.216
## 5 1.151975e-34 4906.951
## 6 5.508625e-34 4907.637
## 65 6.752978e-35 4908.020
## 58 4.292298e-34 4908.136
## 66 3.105320e-34 4908.784
## 12 1.827137e-33 4909.045
## 8 7.219571e-34 4910.902
## 60 7.063736e-34 4910.946
## 68 4.099779e-34 4912.034
## 1 4.545620e-36 4913.416
## 3 2.701218e-35 4913.668
## 2 5.735404e-36 4916.767
## 4 7.916471e-36 4919.928
## 43 3.466838e-38 4926.984
## 41 3.589813e-39 4927.704
## 42 5.455852e-39 4930.683
## 44 9.816090e-39 4933.314
## 51 2.645598e-45 4959.761
## 50 6.299744e-46 4962.631
## 54 4.500331e-46 4963.304
## 55 2.600012e-46 4964.401
## 49 3.536354e-47 4964.575
## 53 3.502839e-47 4964.594
## 14 1.448754e-46 4965.571
## 52 6.930691e-46 4966.246
## 56 1.600591e-46 4969.177
## 21 2.852079e-54 4997.242
## 22 1.120130e-53 4998.321
## 23 2.232406e-54 5001.547
## 24 3.062659e-54 5004.721
## 47 8.082185e-70 5072.657
## 61 2.556701e-71 5075.748
## 13 2.094174e-71 5076.147
## 48 2.382355e-70 5078.906
## 46 1.340888e-71 5080.855
## 63 4.084238e-73 5087.837
## 62 4.008554e-73 5087.875
## 15 3.341638e-73 5088.239
## 45 5.683853e-75 5092.571
## 64 1.012676e-73 5094.432
## 16 1.273137e-75 5103.185
Meilleur modele: MtZoa+G(4)
env$`MtZoa+G(4)`
## pml(tree = `tree_MtZoa+G(4)`, data = data, model = "MtZoa", k = 4,
## shape = 0.829019035772448)
Trouver le meilleur modele
# Cadre 2
env <- attr(modelTest_aa_cadre2, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
modelTest_aa_cadre2[order(modelTest_aa_cadre2$AIC), ]
## Model df logLik AIC AICw AICc
## 46 HIVw+I 62 -5101.986 10327.97 3.618698e-01 10343.72
## 48 HIVw+G(4)+I 63 -5100.988 10327.98 3.613028e-01 10344.27
## 47 HIVw+G(4) 62 -5102.354 10328.71 2.506855e-01 10344.46
## 45 HIVw 61 -5105.614 10333.23 2.614191e-02 10348.45
## 51 HIVb+G(4) 62 -5231.911 10587.82 1.358168e-57 10603.57
## 52 HIVb+G(4)+I 63 -5231.855 10589.71 5.285001e-58 10606.00
## 50 HIVb+I 62 -5235.771 10595.54 2.862673e-59 10611.29
## 49 HIVb 61 -5237.430 10596.86 1.480868e-59 10612.08
## 67 JTT_DCMut+G(4) 62 -5269.726 10663.45 5.129839e-74 10679.20
## 7 JTT+G(4) 62 -5270.491 10664.98 2.387255e-74 10680.73
## 68 JTT_DCMut+G(4)+I 63 -5269.558 10665.12 2.233081e-74 10681.41
## 66 JTT_DCMut+I 62 -5271.007 10666.01 1.425654e-74 10681.76
## 65 JTT_DCMut 61 -5272.287 10666.57 1.077425e-74 10681.79
## 8 JTT+G(4)+I 63 -5270.338 10666.68 1.023273e-74 10682.97
## 6 JTT+I 62 -5271.670 10667.34 7.342263e-75 10683.09
## 5 JTT 61 -5272.829 10667.66 6.263595e-75 10682.88
## 55 FLU+G(4) 62 -5323.252 10770.50 2.912942e-97 10786.25
## 56 FLU+G(4)+I 63 -5323.220 10772.44 1.105422e-97 10788.73
## 54 FLU+I 62 -5328.047 10780.09 2.408802e-99 10795.84
## 53 FLU 61 -5329.737 10781.47 1.208067e-99 10796.69
## 35 mtREV24+G(4) 62 -5453.626 11031.25 6.972729e-154 11047.00
## 36 mtREV24+G(4)+I 63 -5453.627 11033.25 2.561739e-154 11049.55
## 34 mtREV24+I 62 -5476.042 11076.08 1.282787e-163 11091.83
## 33 mtREV24 61 -5477.613 11077.23 7.249972e-164 11092.45
## 23 mtmam+G(4) 62 -5504.986 11133.97 3.451144e-176 11149.72
## 19 cpREV+G(4) 62 -5505.296 11134.59 2.532050e-176 11150.34
## 24 mtmam+G(4)+I 63 -5504.987 11135.97 1.269182e-176 11152.26
## 20 cpREV+G(4)+I 63 -5505.264 11136.53 9.619435e-177 11152.82
## 18 cpREV+I 62 -5515.340 11154.68 1.100233e-180 11170.43
## 17 cpREV 61 -5518.954 11159.91 8.059518e-182 11175.13
## 21 mtmam 61 -5520.483 11162.97 1.745870e-182 11178.19
## 22 mtmam+I 62 -5520.063 11164.13 9.775431e-183 11179.88
## 3 WAG+G(4) 62 -5565.296 11254.59 2.217907e-202 11270.34
## 4 WAG+G(4)+I 63 -5565.296 11256.59 8.158418e-203 11272.88
## 2 WAG+I 62 -5571.499 11267.00 4.485074e-205 11282.75
## 1 WAG 61 -5573.273 11268.55 2.068466e-205 11283.77
## 63 Dayhoff_DCMut+G(4) 62 -5654.327 11432.65 4.786656e-241 11448.40
## 15 Dayhoff+G(4) 62 -5654.700 11433.40 3.297833e-241 11449.15
## 64 Dayhoff_DCMut+G(4)+I 63 -5654.134 11434.27 2.135650e-241 11450.56
## 16 Dayhoff+G(4)+I 63 -5654.509 11435.02 1.467699e-241 11451.31
## 62 Dayhoff_DCMut+I 62 -5661.455 11446.91 3.840960e-244 11462.66
## 14 Dayhoff+I 62 -5661.948 11447.90 2.346654e-244 11463.65
## 61 Dayhoff_DCMut 61 -5666.022 11454.04 1.084507e-245 11469.26
## 13 Dayhoff 61 -5666.569 11455.14 6.274088e-246 11470.36
## 39 VT+G(4) 62 -5701.884 11527.77 1.062507e-261 11543.52
## 40 VT+G(4)+I 63 -5701.862 11529.72 3.994382e-262 11546.02
## 38 VT+I 62 -5713.168 11550.34 1.336383e-266 11566.09
## 37 VT 61 -5715.503 11553.01 3.516087e-267 11568.22
## 59 Blosum62+G(4) 62 -5717.550 11559.10 1.669218e-268 11574.85
## 60 Blosum62+G(4)+I 63 -5717.552 11561.10 6.133079e-269 11577.39
## 11 LG+G(4) 62 -5722.814 11569.63 8.637931e-271 11585.38
## 12 LG+G(4)+I 63 -5722.815 11571.63 3.176634e-271 11587.92
## 57 Blosum62 61 -5725.452 11572.90 1.679169e-271 11588.12
## 58 Blosum62+I 62 -5724.758 11573.52 1.236536e-271 11589.27
## 10 LG+I 62 -5732.276 11588.55 6.720733e-275 11604.30
## 9 LG 61 -5734.226 11590.45 2.597151e-275 11605.67
## 43 RtREV+G(4) 62 -5757.388 11638.78 8.342098e-286 11654.53
## 44 RtREV+G(4)+I 63 -5757.380 11640.76 3.093983e-286 11657.05
## 42 RtREV+I 62 -5770.184 11664.37 2.311155e-291 11680.12
## 41 RtREV 61 -5773.701 11669.40 1.865409e-292 11684.62
## 31 MtZoa+G(4) 62 -5780.309 11684.62 9.266275e-296 11700.37
## 32 MtZoa+G(4)+I 63 -5780.310 11686.62 3.405032e-296 11702.91
## 30 MtZoa+I 62 -5832.736 11789.47 1.577641e-318 11805.22
## 29 MtZoa 61 -5839.378 11800.76 5.592823e-321 11815.98
## 27 mtArt+G(4) 62 -5878.724 11881.45 0.000000e+00 11897.20
## 28 mtArt+G(4)+I 63 -5878.727 11883.45 0.000000e+00 11899.74
## 26 mtArt+I 62 -5976.513 12077.03 0.000000e+00 12092.78
## 25 mtArt 61 -5988.270 12098.54 0.000000e+00 12113.76
## AICcw BIC
## 46 3.923444e-01 10596.19
## 48 2.989025e-01 10600.52
## 47 2.717968e-01 10596.93
## 45 3.695634e-02 10597.12
## 51 1.472545e-57 10856.04
## 52 4.372233e-58 10862.26
## 50 3.103751e-59 10863.76
## 49 2.093477e-59 10860.75
## 67 5.561844e-74 10931.67
## 7 2.588296e-74 10933.20
## 68 1.847408e-74 10937.66
## 66 1.545714e-74 10934.23
## 65 1.523136e-74 10930.47
## 8 8.465441e-75 10939.22
## 6 7.960586e-75 10935.56
## 5 8.854732e-75 10931.55
## 55 3.158254e-97 11038.72
## 56 9.145058e-98 11044.99
## 54 2.611658e-99 11048.31
## 53 1.707823e-99 11045.37
## 35 7.559932e-154 11299.47
## 36 2.119303e-154 11305.80
## 34 1.390816e-163 11344.31
## 33 1.024915e-163 11341.12
## 23 3.741779e-176 11402.19
## 19 2.745285e-176 11402.81
## 24 1.049983e-176 11408.52
## 20 7.958070e-177 11409.07
## 18 1.192888e-180 11422.90
## 17 1.139360e-181 11423.80
## 21 2.468105e-182 11426.86
## 22 1.059866e-182 11432.35
## 3 2.404686e-202 11522.81
## 4 6.749384e-203 11529.14
## 2 4.862781e-205 11535.22
## 1 2.924153e-205 11532.44
## 63 5.189761e-241 11700.88
## 15 3.575557e-241 11701.62
## 64 1.766804e-241 11706.82
## 16 1.214214e-241 11707.57
## 62 4.164423e-244 11715.13
## 14 2.544276e-244 11716.12
## 61 1.533148e-245 11717.94
## 13 8.869565e-246 11719.03
## 39 1.151985e-261 11795.99
## 40 3.304516e-262 11802.27
## 38 1.448925e-266 11818.56
## 37 4.970629e-267 11816.90
## 59 1.809790e-268 11827.32
## 60 5.073839e-269 11833.65
## 11 9.365367e-271 11837.85
## 12 2.628000e-271 11844.18
## 57 2.373811e-271 11836.80
## 58 1.340670e-271 11841.74
## 10 7.286714e-275 11856.77
## 9 3.671545e-275 11854.35
## 43 9.044622e-286 11907.00
## 44 2.559623e-286 11913.31
## 42 2.505787e-291 11932.59
## 41 2.637096e-292 11933.30
## 31 1.004663e-295 11952.84
## 32 2.816951e-296 11959.17
## 30 1.710500e-318 12057.69
## 29 7.905050e-321 12064.65
## 27 0.000000e+00 12149.67
## 28 0.000000e+00 12156.00
## 26 0.000000e+00 12345.25
## 25 0.000000e+00 12362.44
modelTest_aa_cadre2[order(modelTest_aa_cadre2$BIC), ]
## Model df logLik AIC AICw AICc
## 46 HIVw+I 62 -5101.986 10327.97 3.618698e-01 10343.72
## 47 HIVw+G(4) 62 -5102.354 10328.71 2.506855e-01 10344.46
## 45 HIVw 61 -5105.614 10333.23 2.614191e-02 10348.45
## 48 HIVw+G(4)+I 63 -5100.988 10327.98 3.613028e-01 10344.27
## 51 HIVb+G(4) 62 -5231.911 10587.82 1.358168e-57 10603.57
## 49 HIVb 61 -5237.430 10596.86 1.480868e-59 10612.08
## 52 HIVb+G(4)+I 63 -5231.855 10589.71 5.285001e-58 10606.00
## 50 HIVb+I 62 -5235.771 10595.54 2.862673e-59 10611.29
## 65 JTT_DCMut 61 -5272.287 10666.57 1.077425e-74 10681.79
## 5 JTT 61 -5272.829 10667.66 6.263595e-75 10682.88
## 67 JTT_DCMut+G(4) 62 -5269.726 10663.45 5.129839e-74 10679.20
## 7 JTT+G(4) 62 -5270.491 10664.98 2.387255e-74 10680.73
## 66 JTT_DCMut+I 62 -5271.007 10666.01 1.425654e-74 10681.76
## 6 JTT+I 62 -5271.670 10667.34 7.342263e-75 10683.09
## 68 JTT_DCMut+G(4)+I 63 -5269.558 10665.12 2.233081e-74 10681.41
## 8 JTT+G(4)+I 63 -5270.338 10666.68 1.023273e-74 10682.97
## 55 FLU+G(4) 62 -5323.252 10770.50 2.912942e-97 10786.25
## 56 FLU+G(4)+I 63 -5323.220 10772.44 1.105422e-97 10788.73
## 53 FLU 61 -5329.737 10781.47 1.208067e-99 10796.69
## 54 FLU+I 62 -5328.047 10780.09 2.408802e-99 10795.84
## 35 mtREV24+G(4) 62 -5453.626 11031.25 6.972729e-154 11047.00
## 36 mtREV24+G(4)+I 63 -5453.627 11033.25 2.561739e-154 11049.55
## 33 mtREV24 61 -5477.613 11077.23 7.249972e-164 11092.45
## 34 mtREV24+I 62 -5476.042 11076.08 1.282787e-163 11091.83
## 23 mtmam+G(4) 62 -5504.986 11133.97 3.451144e-176 11149.72
## 19 cpREV+G(4) 62 -5505.296 11134.59 2.532050e-176 11150.34
## 24 mtmam+G(4)+I 63 -5504.987 11135.97 1.269182e-176 11152.26
## 20 cpREV+G(4)+I 63 -5505.264 11136.53 9.619435e-177 11152.82
## 18 cpREV+I 62 -5515.340 11154.68 1.100233e-180 11170.43
## 17 cpREV 61 -5518.954 11159.91 8.059518e-182 11175.13
## 21 mtmam 61 -5520.483 11162.97 1.745870e-182 11178.19
## 22 mtmam+I 62 -5520.063 11164.13 9.775431e-183 11179.88
## 3 WAG+G(4) 62 -5565.296 11254.59 2.217907e-202 11270.34
## 4 WAG+G(4)+I 63 -5565.296 11256.59 8.158418e-203 11272.88
## 1 WAG 61 -5573.273 11268.55 2.068466e-205 11283.77
## 2 WAG+I 62 -5571.499 11267.00 4.485074e-205 11282.75
## 63 Dayhoff_DCMut+G(4) 62 -5654.327 11432.65 4.786656e-241 11448.40
## 15 Dayhoff+G(4) 62 -5654.700 11433.40 3.297833e-241 11449.15
## 64 Dayhoff_DCMut+G(4)+I 63 -5654.134 11434.27 2.135650e-241 11450.56
## 16 Dayhoff+G(4)+I 63 -5654.509 11435.02 1.467699e-241 11451.31
## 62 Dayhoff_DCMut+I 62 -5661.455 11446.91 3.840960e-244 11462.66
## 14 Dayhoff+I 62 -5661.948 11447.90 2.346654e-244 11463.65
## 61 Dayhoff_DCMut 61 -5666.022 11454.04 1.084507e-245 11469.26
## 13 Dayhoff 61 -5666.569 11455.14 6.274088e-246 11470.36
## 39 VT+G(4) 62 -5701.884 11527.77 1.062507e-261 11543.52
## 40 VT+G(4)+I 63 -5701.862 11529.72 3.994382e-262 11546.02
## 37 VT 61 -5715.503 11553.01 3.516087e-267 11568.22
## 38 VT+I 62 -5713.168 11550.34 1.336383e-266 11566.09
## 59 Blosum62+G(4) 62 -5717.550 11559.10 1.669218e-268 11574.85
## 60 Blosum62+G(4)+I 63 -5717.552 11561.10 6.133079e-269 11577.39
## 57 Blosum62 61 -5725.452 11572.90 1.679169e-271 11588.12
## 11 LG+G(4) 62 -5722.814 11569.63 8.637931e-271 11585.38
## 58 Blosum62+I 62 -5724.758 11573.52 1.236536e-271 11589.27
## 12 LG+G(4)+I 63 -5722.815 11571.63 3.176634e-271 11587.92
## 9 LG 61 -5734.226 11590.45 2.597151e-275 11605.67
## 10 LG+I 62 -5732.276 11588.55 6.720733e-275 11604.30
## 43 RtREV+G(4) 62 -5757.388 11638.78 8.342098e-286 11654.53
## 44 RtREV+G(4)+I 63 -5757.380 11640.76 3.093983e-286 11657.05
## 42 RtREV+I 62 -5770.184 11664.37 2.311155e-291 11680.12
## 41 RtREV 61 -5773.701 11669.40 1.865409e-292 11684.62
## 31 MtZoa+G(4) 62 -5780.309 11684.62 9.266275e-296 11700.37
## 32 MtZoa+G(4)+I 63 -5780.310 11686.62 3.405032e-296 11702.91
## 30 MtZoa+I 62 -5832.736 11789.47 1.577641e-318 11805.22
## 29 MtZoa 61 -5839.378 11800.76 5.592823e-321 11815.98
## 27 mtArt+G(4) 62 -5878.724 11881.45 0.000000e+00 11897.20
## 28 mtArt+G(4)+I 63 -5878.727 11883.45 0.000000e+00 11899.74
## 26 mtArt+I 62 -5976.513 12077.03 0.000000e+00 12092.78
## 25 mtArt 61 -5988.270 12098.54 0.000000e+00 12113.76
## AICcw BIC
## 46 3.923444e-01 10596.19
## 47 2.717968e-01 10596.93
## 45 3.695634e-02 10597.12
## 48 2.989025e-01 10600.52
## 51 1.472545e-57 10856.04
## 49 2.093477e-59 10860.75
## 52 4.372233e-58 10862.26
## 50 3.103751e-59 10863.76
## 65 1.523136e-74 10930.47
## 5 8.854732e-75 10931.55
## 67 5.561844e-74 10931.67
## 7 2.588296e-74 10933.20
## 66 1.545714e-74 10934.23
## 6 7.960586e-75 10935.56
## 68 1.847408e-74 10937.66
## 8 8.465441e-75 10939.22
## 55 3.158254e-97 11038.72
## 56 9.145058e-98 11044.99
## 53 1.707823e-99 11045.37
## 54 2.611658e-99 11048.31
## 35 7.559932e-154 11299.47
## 36 2.119303e-154 11305.80
## 33 1.024915e-163 11341.12
## 34 1.390816e-163 11344.31
## 23 3.741779e-176 11402.19
## 19 2.745285e-176 11402.81
## 24 1.049983e-176 11408.52
## 20 7.958070e-177 11409.07
## 18 1.192888e-180 11422.90
## 17 1.139360e-181 11423.80
## 21 2.468105e-182 11426.86
## 22 1.059866e-182 11432.35
## 3 2.404686e-202 11522.81
## 4 6.749384e-203 11529.14
## 1 2.924153e-205 11532.44
## 2 4.862781e-205 11535.22
## 63 5.189761e-241 11700.88
## 15 3.575557e-241 11701.62
## 64 1.766804e-241 11706.82
## 16 1.214214e-241 11707.57
## 62 4.164423e-244 11715.13
## 14 2.544276e-244 11716.12
## 61 1.533148e-245 11717.94
## 13 8.869565e-246 11719.03
## 39 1.151985e-261 11795.99
## 40 3.304516e-262 11802.27
## 37 4.970629e-267 11816.90
## 38 1.448925e-266 11818.56
## 59 1.809790e-268 11827.32
## 60 5.073839e-269 11833.65
## 57 2.373811e-271 11836.80
## 11 9.365367e-271 11837.85
## 58 1.340670e-271 11841.74
## 12 2.628000e-271 11844.18
## 9 3.671545e-275 11854.35
## 10 7.286714e-275 11856.77
## 43 9.044622e-286 11907.00
## 44 2.559623e-286 11913.31
## 42 2.505787e-291 11932.59
## 41 2.637096e-292 11933.30
## 31 1.004663e-295 11952.84
## 32 2.816951e-296 11959.17
## 30 1.710500e-318 12057.69
## 29 7.905050e-321 12064.65
## 27 0.000000e+00 12149.67
## 28 0.000000e+00 12156.00
## 26 0.000000e+00 12345.25
## 25 0.000000e+00 12362.44
Meilleur modele: HIVw+I
env$`HIVw+I`
## pml(tree = `tree_HIVw+I`, data = data, model = "HIVw", inv = 0.031773228237453)
Trouver le meilleur modele
# Cadre 3
env <- attr(modelTest_aa_cadre3, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
modelTest_aa_cadre3[order(modelTest_aa_cadre3$AIC), ]
## Model df logLik AIC AICw AICc
## 47 HIVw+G(4) 62 -5274.747 10673.49 6.649646e-01 10690.11
## 48 HIVw+G(4)+I 63 -5274.432 10674.86 3.350351e-01 10692.06
## 46 HIVw+I 62 -5289.262 10702.52 3.303761e-07 10719.14
## 45 HIVw 61 -5296.140 10714.28 9.249019e-10 10730.34
## 23 mtmam+G(4) 62 -5348.536 10821.07 5.978047e-33 10837.69
## 7 JTT+G(4) 62 -5348.833 10821.67 4.440953e-33 10838.29
## 24 mtmam+G(4)+I 63 -5348.536 10823.07 2.198422e-33 10840.27
## 8 JTT+G(4)+I 63 -5348.822 10823.64 1.651017e-33 10840.84
## 6 JTT+I 62 -5357.455 10838.91 7.994553e-37 10855.53
## 67 JTT_DCMut+G(4) 62 -5357.833 10839.67 5.480540e-37 10856.29
## 68 JTT_DCMut+G(4)+I 63 -5357.824 10841.65 2.034288e-37 10858.84
## 5 JTT 61 -5360.294 10842.59 1.271439e-37 10858.65
## 66 JTT_DCMut+I 62 -5366.753 10857.51 7.329049e-41 10874.13
## 65 JTT_DCMut 61 -5369.642 10861.28 1.107470e-41 10877.34
## 55 FLU+G(4) 62 -5372.332 10868.66 2.765310e-43 10885.29
## 56 FLU+G(4)+I 63 -5372.299 10870.60 1.052343e-43 10887.79
## 21 mtmam 61 -5378.721 10879.44 1.263591e-45 10895.50
## 22 mtmam+I 62 -5377.876 10879.75 1.081641e-45 10896.37
## 51 HIVb+G(4) 62 -5386.722 10897.44 1.558350e-49 10914.06
## 52 HIVb+G(4)+I 63 -5386.720 10899.44 5.739467e-50 10916.63
## 54 FLU+I 62 -5398.516 10921.03 1.176533e-54 10937.65
## 50 HIVb+I 62 -5403.549 10931.10 7.665060e-57 10947.72
## 53 FLU 61 -5404.973 10931.95 5.019241e-57 10948.00
## 49 HIVb 61 -5408.020 10938.04 2.383360e-58 10954.10
## 35 mtREV24+G(4) 62 -5437.664 10999.33 1.171223e-71 11015.95
## 36 mtREV24+G(4)+I 63 -5437.664 11001.33 4.307466e-72 11018.52
## 19 cpREV+G(4) 62 -5448.791 11021.58 1.722105e-76 11038.20
## 20 cpREV+G(4)+I 63 -5448.787 11023.57 6.364079e-77 11040.77
## 18 cpREV+I 62 -5470.870 11065.74 4.442382e-86 11082.36
## 34 mtREV24+I 62 -5475.823 11075.65 3.136497e-88 11092.27
## 17 cpREV 61 -5477.362 11076.72 1.830085e-88 11092.78
## 33 mtREV24 61 -5482.664 11087.33 9.109128e-91 11103.39
## 3 WAG+G(4) 62 -5541.009 11206.02 1.536086e-116 11222.64
## 4 WAG+G(4)+I 63 -5541.007 11208.01 5.662926e-117 11225.21
## 2 WAG+I 62 -5551.780 11227.56 3.226686e-121 11244.18
## 1 WAG 61 -5555.198 11232.40 2.874643e-122 11248.46
## 31 MtZoa+G(4) 62 -5563.323 11250.65 3.129609e-126 11267.27
## 32 MtZoa+G(4)+I 63 -5563.324 11252.65 1.150247e-126 11269.84
## 11 LG+G(4) 62 -5596.215 11316.43 1.625238e-140 11333.05
## 12 LG+G(4)+I 63 -5596.215 11318.43 5.978652e-141 11335.62
## 10 LG+I 62 -5610.756 11345.51 7.862243e-147 11362.13
## 9 LG 61 -5614.854 11351.71 3.549742e-148 11367.77
## 63 Dayhoff_DCMut+G(4) 62 -5620.165 11364.33 6.448031e-151 11380.95
## 15 Dayhoff+G(4) 62 -5620.341 11364.68 5.406281e-151 11381.30
## 64 Dayhoff_DCMut+G(4)+I 63 -5620.234 11366.47 2.213188e-151 11383.66
## 16 Dayhoff+G(4)+I 63 -5620.411 11366.82 1.854652e-151 11384.02
## 30 MtZoa+I 62 -5623.709 11371.42 1.864032e-152 11388.04
## 29 MtZoa 61 -5631.963 11385.93 1.317894e-155 11401.99
## 62 Dayhoff_DCMut+I 62 -5637.732 11399.46 1.514287e-158 11416.09
## 14 Dayhoff+I 62 -5638.096 11400.19 1.052591e-158 11416.81
## 61 Dayhoff_DCMut 61 -5641.668 11405.34 8.034959e-160 11421.40
## 13 Dayhoff 61 -5642.067 11406.13 5.393946e-160 11422.19
## 59 Blosum62+G(4) 62 -5715.334 11554.67 3.006953e-192 11571.29
## 60 Blosum62+G(4)+I 63 -5715.306 11556.61 1.137461e-192 11573.81
## 58 Blosum62+I 62 -5725.072 11574.14 1.774557e-196 11590.76
## 57 Blosum62 61 -5729.070 11580.14 8.846016e-198 11596.20
## 27 mtArt+G(4) 62 -5735.987 11595.97 3.224239e-201 11612.60
## 28 mtArt+G(4)+I 63 -5735.988 11597.98 1.184936e-201 11615.17
## 43 RtREV+G(4) 62 -5739.590 11603.18 8.785025e-203 11619.80
## 44 RtREV+G(4)+I 63 -5739.561 11605.12 3.329035e-203 11622.32
## 42 RtREV+I 62 -5754.169 11632.34 4.095275e-209 11648.96
## 41 RtREV 61 -5758.647 11639.29 1.263904e-210 11655.35
## 39 VT+G(4) 62 -5802.941 11729.88 2.696092e-230 11746.50
## 40 VT+G(4)+I 63 -5802.941 11731.88 9.917304e-231 11749.08
## 26 mtArt+I 62 -5825.196 11774.39 5.828761e-240 11791.01
## 25 mtArt 61 -5837.166 11796.33 1.003662e-244 11812.39
## 38 VT+I 62 -5844.255 11812.51 3.077697e-248 11829.13
## 37 VT 61 -5856.713 11835.43 3.251560e-253 11851.49
## AICcw BIC
## 47 7.254928e-01 10938.76
## 48 2.745068e-01 10944.41
## 46 3.604485e-07 10967.79
## 45 1.336380e-09 10975.27
## 23 6.522197e-33 11086.34
## 7 4.845190e-33 11086.93
## 24 1.801250e-33 11092.62
## 8 1.352740e-33 11093.19
## 6 8.722255e-37 11104.18
## 67 5.979405e-37 11104.93
## 68 1.666768e-37 11111.19
## 5 1.837086e-37 11103.58
## 66 7.996174e-41 11122.77
## 65 1.600170e-41 11122.27
## 55 3.017021e-43 11133.93
## 56 8.622239e-44 11140.14
## 21 1.825747e-45 11140.43
## 22 1.180097e-45 11145.02
## 51 1.700198e-49 11162.71
## 52 4.702561e-50 11168.99
## 54 1.283627e-54 11186.30
## 50 8.362770e-57 11196.37
## 53 7.252240e-57 11192.93
## 49 3.443689e-58 11199.03
## 35 1.277833e-71 11264.60
## 36 3.529268e-72 11270.88
## 19 1.878859e-76 11286.85
## 20 5.214329e-77 11293.12
## 18 4.846749e-86 11331.01
## 34 3.421996e-88 11340.91
## 17 2.644268e-88 11337.71
## 33 1.316167e-90 11348.32
## 3 1.675907e-116 11471.29
## 4 4.639848e-117 11477.56
## 2 3.520395e-121 11492.83
## 1 4.153537e-122 11493.39
## 31 3.414481e-126 11515.91
## 32 9.424404e-127 11522.20
## 11 1.773175e-140 11581.70
## 12 4.898533e-141 11587.98
## 10 8.577902e-147 11610.78
## 9 5.128979e-148 11612.70
## 63 7.034961e-151 11629.60
## 15 5.898387e-151 11629.95
## 64 1.813348e-151 11636.02
## 16 1.519586e-151 11636.37
## 30 2.033705e-152 11636.69
## 29 1.904210e-155 11646.92
## 62 1.652125e-158 11664.73
## 14 1.148403e-158 11665.46
## 61 1.160962e-159 11666.33
## 13 7.793648e-160 11667.12
## 59 3.280660e-192 11819.94
## 60 9.319641e-193 11826.16
## 58 1.936085e-196 11839.41
## 57 1.278150e-197 11841.13
## 27 3.517725e-201 11861.24
## 28 9.708622e-202 11867.52
## 43 9.584680e-203 11868.45
## 44 2.727603e-203 11874.67
## 42 4.468047e-209 11897.61
## 41 1.826200e-210 11900.28
## 39 2.941503e-230 11995.15
## 40 8.125619e-231 12001.43
## 26 6.359322e-240 12039.66
## 25 1.450179e-244 12057.32
## 38 3.357843e-248 12077.78
## 37 4.698140e-253 12096.42
modelTest_aa_cadre3[order(modelTest_aa_cadre3$BIC), ]
## Model df logLik AIC AICw AICc
## 47 HIVw+G(4) 62 -5274.747 10673.49 6.649646e-01 10690.11
## 48 HIVw+G(4)+I 63 -5274.432 10674.86 3.350351e-01 10692.06
## 46 HIVw+I 62 -5289.262 10702.52 3.303761e-07 10719.14
## 45 HIVw 61 -5296.140 10714.28 9.249019e-10 10730.34
## 23 mtmam+G(4) 62 -5348.536 10821.07 5.978047e-33 10837.69
## 7 JTT+G(4) 62 -5348.833 10821.67 4.440953e-33 10838.29
## 24 mtmam+G(4)+I 63 -5348.536 10823.07 2.198422e-33 10840.27
## 8 JTT+G(4)+I 63 -5348.822 10823.64 1.651017e-33 10840.84
## 5 JTT 61 -5360.294 10842.59 1.271439e-37 10858.65
## 6 JTT+I 62 -5357.455 10838.91 7.994553e-37 10855.53
## 67 JTT_DCMut+G(4) 62 -5357.833 10839.67 5.480540e-37 10856.29
## 68 JTT_DCMut+G(4)+I 63 -5357.824 10841.65 2.034288e-37 10858.84
## 65 JTT_DCMut 61 -5369.642 10861.28 1.107470e-41 10877.34
## 66 JTT_DCMut+I 62 -5366.753 10857.51 7.329049e-41 10874.13
## 55 FLU+G(4) 62 -5372.332 10868.66 2.765310e-43 10885.29
## 56 FLU+G(4)+I 63 -5372.299 10870.60 1.052343e-43 10887.79
## 21 mtmam 61 -5378.721 10879.44 1.263591e-45 10895.50
## 22 mtmam+I 62 -5377.876 10879.75 1.081641e-45 10896.37
## 51 HIVb+G(4) 62 -5386.722 10897.44 1.558350e-49 10914.06
## 52 HIVb+G(4)+I 63 -5386.720 10899.44 5.739467e-50 10916.63
## 54 FLU+I 62 -5398.516 10921.03 1.176533e-54 10937.65
## 53 FLU 61 -5404.973 10931.95 5.019241e-57 10948.00
## 50 HIVb+I 62 -5403.549 10931.10 7.665060e-57 10947.72
## 49 HIVb 61 -5408.020 10938.04 2.383360e-58 10954.10
## 35 mtREV24+G(4) 62 -5437.664 10999.33 1.171223e-71 11015.95
## 36 mtREV24+G(4)+I 63 -5437.664 11001.33 4.307466e-72 11018.52
## 19 cpREV+G(4) 62 -5448.791 11021.58 1.722105e-76 11038.20
## 20 cpREV+G(4)+I 63 -5448.787 11023.57 6.364079e-77 11040.77
## 18 cpREV+I 62 -5470.870 11065.74 4.442382e-86 11082.36
## 17 cpREV 61 -5477.362 11076.72 1.830085e-88 11092.78
## 34 mtREV24+I 62 -5475.823 11075.65 3.136497e-88 11092.27
## 33 mtREV24 61 -5482.664 11087.33 9.109128e-91 11103.39
## 3 WAG+G(4) 62 -5541.009 11206.02 1.536086e-116 11222.64
## 4 WAG+G(4)+I 63 -5541.007 11208.01 5.662926e-117 11225.21
## 2 WAG+I 62 -5551.780 11227.56 3.226686e-121 11244.18
## 1 WAG 61 -5555.198 11232.40 2.874643e-122 11248.46
## 31 MtZoa+G(4) 62 -5563.323 11250.65 3.129609e-126 11267.27
## 32 MtZoa+G(4)+I 63 -5563.324 11252.65 1.150247e-126 11269.84
## 11 LG+G(4) 62 -5596.215 11316.43 1.625238e-140 11333.05
## 12 LG+G(4)+I 63 -5596.215 11318.43 5.978652e-141 11335.62
## 10 LG+I 62 -5610.756 11345.51 7.862243e-147 11362.13
## 9 LG 61 -5614.854 11351.71 3.549742e-148 11367.77
## 63 Dayhoff_DCMut+G(4) 62 -5620.165 11364.33 6.448031e-151 11380.95
## 15 Dayhoff+G(4) 62 -5620.341 11364.68 5.406281e-151 11381.30
## 64 Dayhoff_DCMut+G(4)+I 63 -5620.234 11366.47 2.213188e-151 11383.66
## 16 Dayhoff+G(4)+I 63 -5620.411 11366.82 1.854652e-151 11384.02
## 30 MtZoa+I 62 -5623.709 11371.42 1.864032e-152 11388.04
## 29 MtZoa 61 -5631.963 11385.93 1.317894e-155 11401.99
## 62 Dayhoff_DCMut+I 62 -5637.732 11399.46 1.514287e-158 11416.09
## 14 Dayhoff+I 62 -5638.096 11400.19 1.052591e-158 11416.81
## 61 Dayhoff_DCMut 61 -5641.668 11405.34 8.034959e-160 11421.40
## 13 Dayhoff 61 -5642.067 11406.13 5.393946e-160 11422.19
## 59 Blosum62+G(4) 62 -5715.334 11554.67 3.006953e-192 11571.29
## 60 Blosum62+G(4)+I 63 -5715.306 11556.61 1.137461e-192 11573.81
## 58 Blosum62+I 62 -5725.072 11574.14 1.774557e-196 11590.76
## 57 Blosum62 61 -5729.070 11580.14 8.846016e-198 11596.20
## 27 mtArt+G(4) 62 -5735.987 11595.97 3.224239e-201 11612.60
## 28 mtArt+G(4)+I 63 -5735.988 11597.98 1.184936e-201 11615.17
## 43 RtREV+G(4) 62 -5739.590 11603.18 8.785025e-203 11619.80
## 44 RtREV+G(4)+I 63 -5739.561 11605.12 3.329035e-203 11622.32
## 42 RtREV+I 62 -5754.169 11632.34 4.095275e-209 11648.96
## 41 RtREV 61 -5758.647 11639.29 1.263904e-210 11655.35
## 39 VT+G(4) 62 -5802.941 11729.88 2.696092e-230 11746.50
## 40 VT+G(4)+I 63 -5802.941 11731.88 9.917304e-231 11749.08
## 26 mtArt+I 62 -5825.196 11774.39 5.828761e-240 11791.01
## 25 mtArt 61 -5837.166 11796.33 1.003662e-244 11812.39
## 38 VT+I 62 -5844.255 11812.51 3.077697e-248 11829.13
## 37 VT 61 -5856.713 11835.43 3.251560e-253 11851.49
## AICcw BIC
## 47 7.254928e-01 10938.76
## 48 2.745068e-01 10944.41
## 46 3.604485e-07 10967.79
## 45 1.336380e-09 10975.27
## 23 6.522197e-33 11086.34
## 7 4.845190e-33 11086.93
## 24 1.801250e-33 11092.62
## 8 1.352740e-33 11093.19
## 5 1.837086e-37 11103.58
## 6 8.722255e-37 11104.18
## 67 5.979405e-37 11104.93
## 68 1.666768e-37 11111.19
## 65 1.600170e-41 11122.27
## 66 7.996174e-41 11122.77
## 55 3.017021e-43 11133.93
## 56 8.622239e-44 11140.14
## 21 1.825747e-45 11140.43
## 22 1.180097e-45 11145.02
## 51 1.700198e-49 11162.71
## 52 4.702561e-50 11168.99
## 54 1.283627e-54 11186.30
## 53 7.252240e-57 11192.93
## 50 8.362770e-57 11196.37
## 49 3.443689e-58 11199.03
## 35 1.277833e-71 11264.60
## 36 3.529268e-72 11270.88
## 19 1.878859e-76 11286.85
## 20 5.214329e-77 11293.12
## 18 4.846749e-86 11331.01
## 17 2.644268e-88 11337.71
## 34 3.421996e-88 11340.91
## 33 1.316167e-90 11348.32
## 3 1.675907e-116 11471.29
## 4 4.639848e-117 11477.56
## 2 3.520395e-121 11492.83
## 1 4.153537e-122 11493.39
## 31 3.414481e-126 11515.91
## 32 9.424404e-127 11522.20
## 11 1.773175e-140 11581.70
## 12 4.898533e-141 11587.98
## 10 8.577902e-147 11610.78
## 9 5.128979e-148 11612.70
## 63 7.034961e-151 11629.60
## 15 5.898387e-151 11629.95
## 64 1.813348e-151 11636.02
## 16 1.519586e-151 11636.37
## 30 2.033705e-152 11636.69
## 29 1.904210e-155 11646.92
## 62 1.652125e-158 11664.73
## 14 1.148403e-158 11665.46
## 61 1.160962e-159 11666.33
## 13 7.793648e-160 11667.12
## 59 3.280660e-192 11819.94
## 60 9.319641e-193 11826.16
## 58 1.936085e-196 11839.41
## 57 1.278150e-197 11841.13
## 27 3.517725e-201 11861.24
## 28 9.708622e-202 11867.52
## 43 9.584680e-203 11868.45
## 44 2.727603e-203 11874.67
## 42 4.468047e-209 11897.61
## 41 1.826200e-210 11900.28
## 39 2.941503e-230 11995.15
## 40 8.125619e-231 12001.43
## 26 6.359322e-240 12039.66
## 25 1.450179e-244 12057.32
## 38 3.357843e-248 12077.78
## 37 4.698140e-253 12096.42
Meilleur modele: HIVw+G(4)
env$`HIVw+G(4)`
## pml(tree = `tree_HIVw+G(4)`, data = data, model = "HIVw", k = 4,
## shape = 3.18746367818674)
Matrice de distances
# Cadre 1
dm_cadre1 <- dist.ml(Align_aa_cadre1_phangorn, model = "MtZoa")
# Cadre 2
dm_cadre2 <- dist.ml(Align_aa_cadre2_phangorn, model = "HIVw")
# Cadre 3
dm_cadre3 <- dist.ml(Align_aa_cadre3_phangorn, model = "HIVw")
Construction d’arbre par NJ
# Cadre 1
treeNJ_cadre1 <- NJ(dm_cadre1)
# Cadre 2
treeNJ_cadre2 <- NJ(dm_cadre2)
# Cadre 3
treeNJ_cadre3 <- NJ(dm_cadre3)
Integration des parametres
# Cadre 1
fit_cadre1 = pml(treeNJ_cadre1, data=Align_aa_cadre1_phangorn)
fitmodel_cadre1 <- update(fit_cadre1, model="MtZoa", k = 4, shape = 0.831043307700432)
fitmodel_cadre1 <- optim.pml(fitmodel_cadre1, model="MtZoa", optShape = TRUE, optGamma = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
# Cadre 2
fit_cadre2 = pml(treeNJ_cadre2, data=Align_aa_cadre2_phangorn)
fitmodel_cadre2 <- update(fit_cadre2, model="HIVw", inv= 0.0317733315974381)
fitmodel_cadre2 <- optim.pml(fitmodel_cadre2, model="HIVw", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
# Cadre 3
fit_cadre3 = pml(treeNJ_cadre3, data=Align_aa_cadre3_phangorn)
fitmodel_cadre3 <- update(fit_cadre3, model="HIVw", k = 4, shape = 3.19289035895832)
fitmodel_cadre3 <- optim.pml(fitmodel_cadre3, model="HIVw", optShape=TRUE, optGamma = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap sans correction
# Cadre 1
boot_cadre1 <- bootstrap.phyDat(Align_aa_cadre1_phangorn, FUN = function(x) NJ(dist.ml(x, model = "MtZoa")), bs = 1000)
cons_boot_cadre1 <- consensus(boot_cadre1, p= 0.5)
plot(cons_boot_cadre1, main = "Bootstrap avec MtZoa pour la cadre 1", no.margin = TRUE)
nodelabels(cons_boot_cadre1$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
# Cadre 2
boot_cadre2 <- bootstrap.phyDat(Align_aa_cadre2_phangorn, FUN = function(x) NJ(dist.ml(x, model = "HIVw")), bs = 1000)
cons_boot_cadre2 <- consensus(boot_cadre2, p= 0.5)
plot(cons_boot_cadre2, main = "Bootstrap avec HIVw pour la cadre 2", no.margin = TRUE)
nodelabels(cons_boot_cadre2$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
# Cadre 3
boot_cadre3 <- bootstrap.phyDat(Align_aa_cadre3_phangorn, FUN = function(x) NJ(dist.ml(x, model = "HIVw")), bs = 1000)
cons_boot_cadre3 <- consensus(boot_cadre3, p= 0.5)
plot(cons_boot_cadre3, main = "Bootstrap avec HIVw pour la cadre 3", no.margin = TRUE)
nodelabels(cons_boot_cadre3$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
Analyse bootstrap avec correction
# Cadre 1
boot_cadre1 = bootstrap.pml(fitmodel_cadre1, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
plotBS(midpoint(fitmodel_cadre1$tree), boot_cadre1, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
# Cadre 2
boot_cadre2 = bootstrap.pml(fitmodel_cadre2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
plotBS(midpoint(fitmodel_cadre2$tree), boot_cadre2, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
# Cadre 3
boot_cadre3 = bootstrap.pml(fitmodel_cadre3, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
plotBS(midpoint(fitmodel_cadre3$tree), boot_cadre3, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Cistude] les ajouter au jeu de donné. Essayer les quatre paires séparément, et ensemble. (ADN et AA)
Modifier les jeux de donnees
##Enlever hippopotame + groupe externe de sequence
myNewSequences <- mySequences[!names(mySequences) %in% c("5836030", "5835009", "157058317", "157058315", "157058313", "157058311", "157058355")]
#Importer le fichier groupe_externe.txt
myExterneSequences <- readDNAStringSet("groupe_externe.txt", format = "fasta")
names(myExterneSequences) <- sub("(^\\S+).*", "\\1", names(myExterneSequences))
Code NCBI: - HQ918430.1 Trichechus manatus voucher - KF430645.1 Dugong dugon voucher
Fusionner avec les cetaces
Sequences_groupe_externe_1 <- c(myNewSequences, myExterneSequences[1:2])
Alignement
mySequences_align_gr_ext_1 = AlignSeqs(Sequences_groupe_externe_1, gapOpening = c(-18,-16), gapExtension = c(-2,-1))
## Determining distance matrix based on shared 9-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Alignment converged - skipping remaining iteration.
Recherche du meilleur modele
mySequences_align_gr_ext_1_ape = as.DNAbin(mySequences_align_gr_ext_1)
mySequences_align_gr_ext_1_phangorn = as.phyDat(mySequences_align_gr_ext_1_ape)
mySequences_gr_ext_1_modelTest = phangorn::modelTest(mySequences_align_gr_ext_1_phangorn)
## Model df logLik AIC BIC
## JC 51 -4344.147 8790.293 9019.243
## JC+I 52 -4059.86 8223.72 8457.158
## JC+G(4) 52 -4068.427 8240.854 8474.293
## JC+G(4)+I 53 -4058.196 8222.392 8460.32
## F81 54 -4314.488 8736.975 8979.392
## F81+I 55 -4017.012 8144.023 8390.929
## F81+G(4) 55 -4024.227 8158.455 8405.361
## F81+G(4)+I 56 -4014.507 8141.014 8392.41
## K80 52 -4009.619 8123.239 8356.677
## K80+I 53 -3660.084 7426.167 7664.095
## K80+G(4) 53 -3669.183 7444.365 7682.293
## K80+G(4)+I 54 -3656.492 7420.984 7663.401
## HKY 55 -3980.945 8071.89 8318.797
## HKY+I 56 -3602.499 7316.999 7568.394
## HKY+G(4) 56 -3617.671 7347.343 7598.738
## HKY+G(4)+I 57 -3599.94 7313.879 7569.764
## TrNe 53 -3982.48 8070.961 8308.889
## TrNe+I 54 -3636.827 7381.654 7624.072
## TrNe+G(4) 54 -3650.48 7408.96 7651.377
## TrNe+G(4)+I 55 -3632.633 7375.265 7622.171
## TrN 56 -3973.238 8058.476 8309.871
## TrN+I 57 -3600.693 7315.386 7571.27
## TrN+G(4) 57 -3615.921 7345.843 7601.727
## TrN+G(4)+I 58 -3597.709 7311.418 7571.792
## TPM1 53 -4009.619 8125.238 8363.166
## TPM1+I 54 -3659.721 7427.442 7669.859
## TPM1+G(4) 54 -3668.589 7445.178 7687.595
## TPM1+G(4)+I 55 -3655.97 7421.939 7668.845
## K81 53 -4009.619 8125.238 8363.166
## K81+I 54 -3659.721 7427.442 7669.859
## K81+G(4) 54 -3668.589 7445.178 7687.595
## K81+G(4)+I 55 -3655.97 7421.939 7668.845
## TPM1u 56 -3980.936 8073.872 8325.268
## TPM1u+I 57 -3601.942 7317.884 7573.769
## TPM1u+G(4) 57 -3616.896 7347.793 7603.677
## TPM1u+G(4)+I 58 -3599.252 7314.503 7574.877
## TPM2 53 -3978.025 8062.049 8299.977
## TPM2+I 54 -3652.455 7412.91 7655.327
## TPM2+G(4) 54 -3657.53 7423.059 7665.476
## TPM2+G(4)+I 55 -3647.626 7405.252 7652.158
## TPM2u 56 -3959.441 8030.882 8282.278
## TPM2u+I 57 -3599.831 7313.662 7569.547
## TPM2u+G(4) 57 -3614.478 7342.956 7598.841
## TPM2u+G(4)+I 58 -3597.244 7310.489 7570.863
## TPM3 53 -4009.324 8124.648 8362.576
## TPM3+I 54 -3653.62 7415.239 7657.656
## TPM3+G(4) 54 -3664.871 7437.742 7680.159
## TPM3+G(4)+I 55 -3649.949 7409.897 7656.804
## TPM3u 56 -3980.797 8073.594 8324.989
## TPM3u+I 57 -3596.915 7307.831 7563.715
## TPM3u+G(4) 57 -3613.728 7341.455 7597.34
## TPM3u+G(4)+I 58 -3594.204 7304.409 7564.783
## TIM1e 54 -3982.48 8072.96 8315.377
## TIM1e+I 55 -3636.449 7382.897 7629.803
## TIM1e+G(4) 55 -3649.767 7409.533 7656.44
## TIM1e+G(4)+I 56 -3632.112 7376.224 7627.62
## TIM1 57 -3973.229 8060.459 8316.343
## TIM1+I 58 -3600.137 7316.274 7576.648
## TIM1+G(4) 58 -3615.119 7346.238 7606.612
## TIM1+G(4)+I 59 -3597.02 7312.04 7576.903
## TIM2e 54 -3950.763 8009.526 8251.943
## TIM2e+I 55 -3626.819 7363.638 7610.544
## TIM2e+G(4) 55 -3638.398 7386.796 7633.702
## TIM2e+G(4)+I 56 -3621.474 7354.948 7606.344
## TIM2 57 -3951.784 8017.568 8273.453
## TIM2+I 58 -3597.782 7311.564 7571.938
## TIM2+G(4) 58 -3612.49 7340.98 7601.354
## TIM2+G(4)+I 59 -3594.73 7307.461 7572.324
## TIM3e 54 -3982.132 8072.264 8314.681
## TIM3e+I 55 -3629.973 7369.946 7616.852
## TIM3e+G(4) 55 -3645.669 7401.338 7648.244
## TIM3e+G(4)+I 56 -3625.53 7363.06 7614.455
## TIM3 57 -3973.069 8060.138 8316.023
## TIM3+I 58 -3594.999 7305.997 7566.371
## TIM3+G(4) 58 -3611.859 7339.717 7600.091
## TIM3+G(4)+I 59 -3591.802 7301.604 7566.467
## TVMe 55 -3976.644 8063.287 8310.194
## TVMe+I 56 -3645.028 7402.056 7653.452
## TVMe+G(4) 56 -3652.83 7417.659 7669.055
## TVMe+G(4)+I 57 -3640.697 7395.394 7651.278
## TVM 58 -3958.2 8032.401 8292.775
## TVM+I 59 -3593.031 7304.062 7568.925
## TVM+G(4) 59 -3610.178 7338.357 7603.22
## TVM+G(4)+I 60 -3590.584 7301.169 7570.521
## SYM 56 -3949.43 8010.86 8262.256
## SYM+I 57 -3619.025 7352.05 7607.935
## SYM+G(4) 57 -3633.334 7380.668 7636.552
## SYM+G(4)+I 58 -3614.117 7344.235 7604.609
## GTR 59 -3950.578 8019.156 8284.019
## GTR+I 60 -3590.889 7301.778 7571.13
## GTR+G(4) 60 -3608.088 7336.176 7605.528
## GTR+G(4)+I 61 -3587.971 7297.943 7571.784
Trouver le meilleur modele
env <- attr(mySequences_gr_ext_1_modelTest, "env")
ls(env=env)
## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"
mySequences_gr_ext_1_modelTest[order(mySequences_gr_ext_1_modelTest$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 61 -3587.971 7297.943 6.124032e-01 7310.634 5.273579e-01
## 84 TVM+G(4)+I 60 -3590.584 7301.169 1.220580e-01 7313.430 1.303169e-01
## 76 TIM3+G(4)+I 59 -3591.802 7301.604 9.818093e-02 7313.443 1.294385e-01
## 90 GTR+I 60 -3590.889 7301.778 9.001916e-02 7314.039 9.611019e-02
## 82 TVM+I 59 -3593.031 7304.062 2.872422e-02 7315.902 3.786906e-02
## 52 TPM3u+G(4)+I 58 -3594.204 7304.409 2.415417e-02 7315.834 3.916284e-02
## 74 TIM3+I 58 -3594.999 7305.997 1.091535e-02 7317.423 1.769783e-02
## 68 TIM2+G(4)+I 59 -3594.730 7307.461 5.250979e-03 7319.300 6.922716e-03
## 50 TPM3u+I 57 -3596.915 7307.831 4.364673e-03 7318.851 8.668272e-03
## 44 TPM2u+G(4)+I 58 -3597.244 7310.489 1.155354e-03 7321.915 1.873255e-03
## 24 TrN+G(4)+I 58 -3597.709 7311.418 7.260973e-04 7322.843 1.177272e-03
## 66 TIM2+I 58 -3597.782 7311.564 6.750246e-04 7322.989 1.094465e-03
## 60 TIM1+G(4)+I 59 -3597.020 7312.040 5.319853e-04 7323.879 7.013518e-04
## 42 TPM2u+I 57 -3599.831 7313.662 2.364295e-04 7324.682 4.695506e-04
## 16 HKY+G(4)+I 57 -3599.940 7313.879 2.120983e-04 7324.899 4.212287e-04
## 36 TPM1u+G(4)+I 58 -3599.252 7314.503 1.552180e-04 7325.929 2.516659e-04
## 22 TrN+I 57 -3600.693 7315.386 9.985248e-05 7326.406 1.983077e-04
## 58 TIM1+I 58 -3600.137 7316.274 6.402913e-05 7327.700 1.038149e-04
## 14 HKY+I 56 -3602.499 7316.999 4.457273e-05 7327.621 1.079967e-04
## 34 TPM1u+I 57 -3601.942 7317.884 2.863049e-05 7328.904 5.686036e-05
## 91 GTR+G(4) 60 -3608.088 7336.176 3.054235e-09 7348.437 3.260896e-09
## 83 TVM+G(4) 59 -3610.178 7338.357 1.026185e-09 7350.196 1.352889e-09
## 75 TIM3+G(4) 58 -3611.859 7339.717 5.198323e-10 7351.143 8.428404e-10
## 67 TIM2+G(4) 58 -3612.490 7340.980 2.764645e-10 7352.406 4.482512e-10
## 51 TPM3u+G(4) 57 -3613.728 7341.455 2.179732e-10 7352.475 4.328964e-10
## 43 TPM2u+G(4) 57 -3614.478 7342.956 1.029133e-10 7353.976 2.043865e-10
## 88 SYM+G(4)+I 58 -3614.117 7344.235 5.431292e-11 7355.660 8.806134e-11
## 23 TrN+G(4) 57 -3615.921 7345.843 2.430675e-11 7356.863 4.827337e-11
## 59 TIM1+G(4) 58 -3615.119 7346.238 1.994396e-11 7357.664 3.233653e-11
## 15 HKY+G(4) 56 -3617.671 7347.343 1.148019e-11 7357.965 2.781571e-11
## 35 TPM1u+G(4) 57 -3616.896 7347.793 9.168449e-12 7358.813 1.820860e-11
## 86 SYM+I 57 -3619.025 7352.050 1.091058e-12 7363.070 2.166849e-12
## 64 TIM2e+G(4)+I 56 -3621.474 7354.948 2.561579e-13 7365.570 6.206531e-13
## 72 TIM3e+G(4)+I 56 -3625.530 7363.060 4.436780e-15 7373.682 1.075001e-14
## 62 TIM2e+I 55 -3626.819 7363.638 3.323520e-15 7373.870 9.785204e-15
## 70 TIM3e+I 55 -3629.973 7369.946 1.418189e-16 7380.179 4.175472e-16
## 20 TrNe+G(4)+I 55 -3632.633 7375.265 9.925204e-18 7385.498 2.922208e-17
## 56 TIM1e+G(4)+I 56 -3632.112 7376.224 6.143559e-18 7386.847 1.488542e-17
## 87 SYM+G(4) 57 -3633.334 7380.668 6.661986e-19 7391.688 1.323075e-18
## 18 TrNe+I 54 -3636.827 7381.654 4.067102e-19 7391.505 1.449326e-18
## 54 TIM1e+I 55 -3636.449 7382.897 2.184939e-19 7393.130 6.432961e-19
## 63 TIM2e+G(4) 55 -3638.398 7386.796 3.110886e-20 7397.028 9.159161e-20
## 80 TVMe+G(4)+I 57 -3640.697 7395.394 4.225317e-22 7406.414 8.391509e-22
## 71 TIM3e+G(4) 55 -3645.669 7401.338 2.162868e-23 7411.571 6.367979e-23
## 78 TVMe+I 56 -3645.028 7402.056 1.510402e-23 7412.679 3.659601e-23
## 40 TPM2+G(4)+I 55 -3647.626 7405.252 3.055831e-24 7415.485 8.997066e-24
## 19 TrNe+G(4) 54 -3650.480 7408.960 4.784941e-25 7418.811 1.705130e-24
## 55 TIM1e+G(4) 55 -3649.767 7409.533 3.593143e-25 7419.766 1.057904e-24
## 48 TPM3+G(4)+I 55 -3649.949 7409.897 2.995047e-25 7420.130 8.818106e-25
## 38 TPM2+I 54 -3652.455 7412.910 6.639785e-26 7422.761 2.366111e-25
## 46 TPM3+I 54 -3653.620 7415.239 2.072258e-26 7425.090 7.384562e-26
## 79 TVMe+G(4) 56 -3652.830 7417.659 6.179642e-27 7428.281 1.497285e-26
## 12 K80+G(4)+I 54 -3656.492 7420.984 1.172001e-27 7430.835 4.176466e-27
## 28 TPM1+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 32 K81+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 39 TPM2+G(4) 54 -3657.530 7423.059 4.153240e-28 7432.910 1.480022e-27
## 10 K80+I 53 -3660.084 7426.167 8.780130e-29 7435.644 3.772061e-28
## 26 TPM1+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 30 K81+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 47 TPM3+G(4) 54 -3664.871 7437.742 2.692252e-31 7447.592 9.593935e-31
## 11 K80+G(4) 53 -3669.183 7444.365 9.812151e-33 7453.842 4.215432e-32
## 27 TPM1+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 31 K81+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 61 TIM2e 54 -3950.763 8009.526 1.856973e-155 8019.376 6.617388e-155
## 85 SYM 56 -3949.430 8010.860 9.528525e-156 8021.482 2.308696e-155
## 65 TIM2 57 -3951.784 8017.568 3.330033e-157 8028.588 6.613469e-157
## 89 GTR 59 -3950.578 8019.156 1.504917e-157 8030.996 1.984033e-157
## 41 TPM2u 56 -3959.441 8030.882 4.277783e-160 8041.505 1.036477e-159
## 81 TVM 58 -3958.200 8032.401 2.002303e-160 8043.826 3.246473e-160
## 21 TrN 56 -3973.238 8058.476 4.358826e-166 8069.098 1.056114e-165
## 73 TIM3 57 -3973.069 8060.138 1.898376e-166 8071.158 3.770188e-166
## 57 TIM1 57 -3973.229 8060.459 1.617371e-166 8071.479 3.212110e-166
## 37 TPM2 53 -3978.025 8062.049 7.302601e-167 8071.526 3.137295e-166
## 77 TVMe 55 -3976.644 8063.287 3.931877e-167 8073.520 1.157635e-166
## 17 TrNe 53 -3982.480 8070.961 8.478992e-169 8080.438 3.642689e-168
## 13 HKY 55 -3980.945 8071.890 5.326671e-169 8082.123 1.568294e-168
## 69 TIM3e 54 -3982.132 8072.264 4.419060e-169 8082.115 1.574747e-168
## 53 TIM1e 54 -3982.480 8072.960 3.120240e-169 8082.811 1.111908e-168
## 49 TPM3u 56 -3980.797 8073.594 2.272693e-169 8084.216 5.506578e-169
## 33 TPM1u 56 -3980.936 8073.872 1.977647e-169 8084.494 4.791704e-169
## 9 K80 52 -4009.619 8123.239 3.769941e-180 8132.349 1.944935e-179
## 45 TPM3 53 -4009.324 8124.648 1.863147e-180 8134.125 8.004330e-180
## 25 TPM1 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 29 K81 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 8 F81+G(4)+I 56 -4014.507 8141.014 5.204601e-184 8151.637 1.261039e-183
## 6 F81+I 55 -4017.012 8144.023 1.156244e-184 8154.256 3.404248e-184
## 7 F81+G(4) 55 -4024.227 8158.455 8.496664e-188 8168.687 2.501613e-187
## 4 JC+G(4)+I 53 -4058.196 8222.392 1.110371e-201 8231.869 4.770304e-201
## 2 JC+I 52 -4059.860 8223.720 5.716742e-202 8232.830 2.949301e-201
## 3 JC+G(4) 52 -4068.427 8240.854 1.087487e-205 8249.965 5.610409e-205
## 5 F81 54 -4314.488 8736.975 2.018815e-313 8746.826 7.194117e-313
## 1 JC 51 -4344.147 8790.293 0.000000e+00 8799.046 4.940656e-324
## BIC
## 92 7571.784
## 84 7570.521
## 76 7566.467
## 90 7571.130
## 82 7568.925
## 52 7564.783
## 74 7566.371
## 68 7572.324
## 50 7563.715
## 44 7570.863
## 24 7571.792
## 66 7571.938
## 60 7576.903
## 42 7569.547
## 16 7569.764
## 36 7574.877
## 22 7571.270
## 58 7576.648
## 14 7568.394
## 34 7573.769
## 91 7605.528
## 83 7603.220
## 75 7600.091
## 67 7601.354
## 51 7597.340
## 43 7598.841
## 88 7604.609
## 23 7601.727
## 59 7606.612
## 15 7598.738
## 35 7603.677
## 86 7607.935
## 64 7606.344
## 72 7614.455
## 62 7610.544
## 70 7616.852
## 20 7622.171
## 56 7627.620
## 87 7636.552
## 18 7624.072
## 54 7629.803
## 63 7633.702
## 80 7651.278
## 71 7648.244
## 78 7653.452
## 40 7652.158
## 19 7651.377
## 55 7656.440
## 48 7656.804
## 38 7655.327
## 46 7657.656
## 79 7669.055
## 12 7663.401
## 28 7668.845
## 32 7668.845
## 39 7665.476
## 10 7664.095
## 26 7669.859
## 30 7669.859
## 47 7680.159
## 11 7682.293
## 27 7687.595
## 31 7687.595
## 61 8251.943
## 85 8262.256
## 65 8273.453
## 89 8284.019
## 41 8282.278
## 81 8292.775
## 21 8309.871
## 73 8316.023
## 57 8316.343
## 37 8299.977
## 77 8310.194
## 17 8308.889
## 13 8318.797
## 69 8314.681
## 53 8315.377
## 49 8324.989
## 33 8325.268
## 9 8356.677
## 45 8362.576
## 25 8363.166
## 29 8363.166
## 8 8392.410
## 6 8390.929
## 7 8405.361
## 4 8460.320
## 2 8457.158
## 3 8474.293
## 5 8979.392
## 1 9019.243
mySequences_gr_ext_1_modelTest[order(mySequences_gr_ext_1_modelTest$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 50 TPM3u+I 57 -3596.915 7307.831 4.364673e-03 7318.851 8.668272e-03
## 52 TPM3u+G(4)+I 58 -3594.204 7304.409 2.415417e-02 7315.834 3.916284e-02
## 74 TIM3+I 58 -3594.999 7305.997 1.091535e-02 7317.423 1.769783e-02
## 76 TIM3+G(4)+I 59 -3591.802 7301.604 9.818093e-02 7313.443 1.294385e-01
## 14 HKY+I 56 -3602.499 7316.999 4.457273e-05 7327.621 1.079967e-04
## 82 TVM+I 59 -3593.031 7304.062 2.872422e-02 7315.902 3.786906e-02
## 42 TPM2u+I 57 -3599.831 7313.662 2.364295e-04 7324.682 4.695506e-04
## 16 HKY+G(4)+I 57 -3599.940 7313.879 2.120983e-04 7324.899 4.212287e-04
## 84 TVM+G(4)+I 60 -3590.584 7301.169 1.220580e-01 7313.430 1.303169e-01
## 44 TPM2u+G(4)+I 58 -3597.244 7310.489 1.155354e-03 7321.915 1.873255e-03
## 90 GTR+I 60 -3590.889 7301.778 9.001916e-02 7314.039 9.611019e-02
## 22 TrN+I 57 -3600.693 7315.386 9.985248e-05 7326.406 1.983077e-04
## 92 GTR+G(4)+I 61 -3587.971 7297.943 6.124032e-01 7310.634 5.273579e-01
## 24 TrN+G(4)+I 58 -3597.709 7311.418 7.260973e-04 7322.843 1.177272e-03
## 66 TIM2+I 58 -3597.782 7311.564 6.750246e-04 7322.989 1.094465e-03
## 68 TIM2+G(4)+I 59 -3594.730 7307.461 5.250979e-03 7319.300 6.922716e-03
## 34 TPM1u+I 57 -3601.942 7317.884 2.863049e-05 7328.904 5.686036e-05
## 36 TPM1u+G(4)+I 58 -3599.252 7314.503 1.552180e-04 7325.929 2.516659e-04
## 58 TIM1+I 58 -3600.137 7316.274 6.402913e-05 7327.700 1.038149e-04
## 60 TIM1+G(4)+I 59 -3597.020 7312.040 5.319853e-04 7323.879 7.013518e-04
## 51 TPM3u+G(4) 57 -3613.728 7341.455 2.179732e-10 7352.475 4.328964e-10
## 15 HKY+G(4) 56 -3617.671 7347.343 1.148019e-11 7357.965 2.781571e-11
## 43 TPM2u+G(4) 57 -3614.478 7342.956 1.029133e-10 7353.976 2.043865e-10
## 75 TIM3+G(4) 58 -3611.859 7339.717 5.198323e-10 7351.143 8.428404e-10
## 67 TIM2+G(4) 58 -3612.490 7340.980 2.764645e-10 7352.406 4.482512e-10
## 23 TrN+G(4) 57 -3615.921 7345.843 2.430675e-11 7356.863 4.827337e-11
## 83 TVM+G(4) 59 -3610.178 7338.357 1.026185e-09 7350.196 1.352889e-09
## 35 TPM1u+G(4) 57 -3616.896 7347.793 9.168449e-12 7358.813 1.820860e-11
## 88 SYM+G(4)+I 58 -3614.117 7344.235 5.431292e-11 7355.660 8.806134e-11
## 91 GTR+G(4) 60 -3608.088 7336.176 3.054235e-09 7348.437 3.260896e-09
## 64 TIM2e+G(4)+I 56 -3621.474 7354.948 2.561579e-13 7365.570 6.206531e-13
## 59 TIM1+G(4) 58 -3615.119 7346.238 1.994396e-11 7357.664 3.233653e-11
## 86 SYM+I 57 -3619.025 7352.050 1.091058e-12 7363.070 2.166849e-12
## 62 TIM2e+I 55 -3626.819 7363.638 3.323520e-15 7373.870 9.785204e-15
## 72 TIM3e+G(4)+I 56 -3625.530 7363.060 4.436780e-15 7373.682 1.075001e-14
## 70 TIM3e+I 55 -3629.973 7369.946 1.418189e-16 7380.179 4.175472e-16
## 20 TrNe+G(4)+I 55 -3632.633 7375.265 9.925204e-18 7385.498 2.922208e-17
## 18 TrNe+I 54 -3636.827 7381.654 4.067102e-19 7391.505 1.449326e-18
## 56 TIM1e+G(4)+I 56 -3632.112 7376.224 6.143559e-18 7386.847 1.488542e-17
## 54 TIM1e+I 55 -3636.449 7382.897 2.184939e-19 7393.130 6.432961e-19
## 63 TIM2e+G(4) 55 -3638.398 7386.796 3.110886e-20 7397.028 9.159161e-20
## 87 SYM+G(4) 57 -3633.334 7380.668 6.661986e-19 7391.688 1.323075e-18
## 71 TIM3e+G(4) 55 -3645.669 7401.338 2.162868e-23 7411.571 6.367979e-23
## 80 TVMe+G(4)+I 57 -3640.697 7395.394 4.225317e-22 7406.414 8.391509e-22
## 19 TrNe+G(4) 54 -3650.480 7408.960 4.784941e-25 7418.811 1.705130e-24
## 40 TPM2+G(4)+I 55 -3647.626 7405.252 3.055831e-24 7415.485 8.997066e-24
## 78 TVMe+I 56 -3645.028 7402.056 1.510402e-23 7412.679 3.659601e-23
## 38 TPM2+I 54 -3652.455 7412.910 6.639785e-26 7422.761 2.366111e-25
## 55 TIM1e+G(4) 55 -3649.767 7409.533 3.593143e-25 7419.766 1.057904e-24
## 48 TPM3+G(4)+I 55 -3649.949 7409.897 2.995047e-25 7420.130 8.818106e-25
## 46 TPM3+I 54 -3653.620 7415.239 2.072258e-26 7425.090 7.384562e-26
## 12 K80+G(4)+I 54 -3656.492 7420.984 1.172001e-27 7430.835 4.176466e-27
## 10 K80+I 53 -3660.084 7426.167 8.780130e-29 7435.644 3.772061e-28
## 39 TPM2+G(4) 54 -3657.530 7423.059 4.153240e-28 7432.910 1.480022e-27
## 28 TPM1+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 32 K81+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 79 TVMe+G(4) 56 -3652.830 7417.659 6.179642e-27 7428.281 1.497285e-26
## 26 TPM1+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 30 K81+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 47 TPM3+G(4) 54 -3664.871 7437.742 2.692252e-31 7447.592 9.593935e-31
## 11 K80+G(4) 53 -3669.183 7444.365 9.812151e-33 7453.842 4.215432e-32
## 27 TPM1+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 31 K81+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 61 TIM2e 54 -3950.763 8009.526 1.856973e-155 8019.376 6.617388e-155
## 85 SYM 56 -3949.430 8010.860 9.528525e-156 8021.482 2.308696e-155
## 65 TIM2 57 -3951.784 8017.568 3.330033e-157 8028.588 6.613469e-157
## 41 TPM2u 56 -3959.441 8030.882 4.277783e-160 8041.505 1.036477e-159
## 89 GTR 59 -3950.578 8019.156 1.504917e-157 8030.996 1.984033e-157
## 81 TVM 58 -3958.200 8032.401 2.002303e-160 8043.826 3.246473e-160
## 37 TPM2 53 -3978.025 8062.049 7.302601e-167 8071.526 3.137295e-166
## 17 TrNe 53 -3982.480 8070.961 8.478992e-169 8080.438 3.642689e-168
## 21 TrN 56 -3973.238 8058.476 4.358826e-166 8069.098 1.056114e-165
## 77 TVMe 55 -3976.644 8063.287 3.931877e-167 8073.520 1.157635e-166
## 69 TIM3e 54 -3982.132 8072.264 4.419060e-169 8082.115 1.574747e-168
## 53 TIM1e 54 -3982.480 8072.960 3.120240e-169 8082.811 1.111908e-168
## 73 TIM3 57 -3973.069 8060.138 1.898376e-166 8071.158 3.770188e-166
## 57 TIM1 57 -3973.229 8060.459 1.617371e-166 8071.479 3.212110e-166
## 13 HKY 55 -3980.945 8071.890 5.326671e-169 8082.123 1.568294e-168
## 49 TPM3u 56 -3980.797 8073.594 2.272693e-169 8084.216 5.506578e-169
## 33 TPM1u 56 -3980.936 8073.872 1.977647e-169 8084.494 4.791704e-169
## 9 K80 52 -4009.619 8123.239 3.769941e-180 8132.349 1.944935e-179
## 45 TPM3 53 -4009.324 8124.648 1.863147e-180 8134.125 8.004330e-180
## 25 TPM1 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 29 K81 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 6 F81+I 55 -4017.012 8144.023 1.156244e-184 8154.256 3.404248e-184
## 8 F81+G(4)+I 56 -4014.507 8141.014 5.204601e-184 8151.637 1.261039e-183
## 7 F81+G(4) 55 -4024.227 8158.455 8.496664e-188 8168.687 2.501613e-187
## 2 JC+I 52 -4059.860 8223.720 5.716742e-202 8232.830 2.949301e-201
## 4 JC+G(4)+I 53 -4058.196 8222.392 1.110371e-201 8231.869 4.770304e-201
## 3 JC+G(4) 52 -4068.427 8240.854 1.087487e-205 8249.965 5.610409e-205
## 5 F81 54 -4314.488 8736.975 2.018815e-313 8746.826 7.194117e-313
## 1 JC 51 -4344.147 8790.293 0.000000e+00 8799.046 4.940656e-324
## BIC
## 50 7563.715
## 52 7564.783
## 74 7566.371
## 76 7566.467
## 14 7568.394
## 82 7568.925
## 42 7569.547
## 16 7569.764
## 84 7570.521
## 44 7570.863
## 90 7571.130
## 22 7571.270
## 92 7571.784
## 24 7571.792
## 66 7571.938
## 68 7572.324
## 34 7573.769
## 36 7574.877
## 58 7576.648
## 60 7576.903
## 51 7597.340
## 15 7598.738
## 43 7598.841
## 75 7600.091
## 67 7601.354
## 23 7601.727
## 83 7603.220
## 35 7603.677
## 88 7604.609
## 91 7605.528
## 64 7606.344
## 59 7606.612
## 86 7607.935
## 62 7610.544
## 72 7614.455
## 70 7616.852
## 20 7622.171
## 18 7624.072
## 56 7627.620
## 54 7629.803
## 63 7633.702
## 87 7636.552
## 71 7648.244
## 80 7651.278
## 19 7651.377
## 40 7652.158
## 78 7653.452
## 38 7655.327
## 55 7656.440
## 48 7656.804
## 46 7657.656
## 12 7663.401
## 10 7664.095
## 39 7665.476
## 28 7668.845
## 32 7668.845
## 79 7669.055
## 26 7669.859
## 30 7669.859
## 47 7680.159
## 11 7682.293
## 27 7687.595
## 31 7687.595
## 61 8251.943
## 85 8262.256
## 65 8273.453
## 41 8282.278
## 89 8284.019
## 81 8292.775
## 37 8299.977
## 17 8308.889
## 21 8309.871
## 77 8310.194
## 69 8314.681
## 53 8315.377
## 73 8316.023
## 57 8316.343
## 13 8318.797
## 49 8324.989
## 33 8325.268
## 9 8356.677
## 45 8362.576
## 25 8363.166
## 29 8363.166
## 6 8390.929
## 8 8392.410
## 7 8405.361
## 2 8457.158
## 4 8460.320
## 3 8474.293
## 5 8979.392
## 1 9019.243
Meilleur modele: TIM3+G(4)+I
env$`TIM3+G(4)+I`
## pml(tree = `tree_TIM3+G(4)+I`, data = data, bf = c(0.267772915837927,
## 0.26993237483662, 0.170199465818037, 0.292095243507416), Q = c(0.216488832975341,
## 10.4697492964762, 1, 0.216488832975341, 14.0840108381235, 1),
## model = "TIM3", inv = 0.600116676053066, k = 4, shape = 5.33821822461735)
Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_1 = dist.dna(mySequences_align_gr_ext_1_ape, pairwise.deletion=FALSE, model="TN93") # TIM3 existe pas donc utilise un modele similaire
# Construction arbre NJ
treeNJ_gr_ext_1 <- NJ(mySequences_align_gr_ext_1)
# Visualisation
plot(treeNJ_gr_ext_1, main="Arbre NJ Groupe externe 1")
Integration des parametres
fit_gr_ext_1 = pml(treeNJ_gr_ext_1, data=mySequences_align_gr_ext_1_phangorn)
fitTIM3_gr_ext_1 <- update(fit_gr_ext_1, model="TIM3", k=4, inv=0.600116108726824, shape=5.33769016071792)
fitTIM3_gr_ext_1 <- optim.pml(fitTIM3_gr_ext_1, model="TIM3", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_gr_ext_1 = bootstrap.pml(fitTIM3_gr_ext_1, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTIM3_gr_ext_1$tree), bs_gr_ext_1, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Alignement
mySequences_align_aa_gr_ext_1 = AlignTranslation(Sequences_groupe_externe_1,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.04 secs
##
## Alignment converged - skipping remaining iteration.
Conversion
mySequences_align_aa_gr_ext_1_ape = as.AAbin(mySequences_align_aa_gr_ext_1)
mySequences_align_aa_gr_ext_1_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_1_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
Recherche du meilleur modele
mySequences_align_aa_gr_ext_1_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_1_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 51 -788.1395 1678.279 1850.182
## WAG+I 52 -780.0185 1664.037 1839.31
## WAG+G(4) 52 -780.9756 1665.951 1841.224
## WAG+G(4)+I 53 -780.1385 1666.277 1844.921
## JTT 51 -785.7615 1673.523 1845.426
## JTT+I 52 -777.8272 1659.654 1834.928
## JTT+G(4) 52 -778.7116 1661.423 1836.696
## JTT+G(4)+I 53 -777.9091 1661.818 1840.462
## LG 51 -784.6328 1671.266 1843.168
## LG+I 52 -777.2918 1658.584 1833.857
## LG+G(4) 52 -777.9279 1659.856 1835.129
## LG+G(4)+I 53 -777.3025 1660.605 1839.249
## Dayhoff 51 -798.247 1698.494 1870.397
## Dayhoff+I 52 -789.6021 1683.204 1858.477
## Dayhoff+G(4) 52 -790.7679 1685.536 1860.809
## Dayhoff+G(4)+I 53 -789.7597 1685.519 1864.163
## cpREV 51 -776.6083 1655.217 1827.119
## cpREV+I 52 -768.4012 1640.802 1816.076
## cpREV+G(4) 52 -769.3804 1642.761 1818.034
## cpREV+G(4)+I 53 -768.412 1642.824 1821.468
## mtmam 51 -749.5626 1601.125 1773.028
## mtmam+I 52 -743.835 1591.67 1766.943
## mtmam+G(4) 52 -743.9617 1591.923 1767.197
## mtmam+G(4)+I 53 -743.8491 1593.698 1772.342
## mtArt 51 -751.6583 1605.317 1777.219
## mtArt+I 52 -745.7645 1595.529 1770.802
## mtArt+G(4) 52 -745.9259 1595.852 1771.125
## mtArt+G(4)+I 53 -745.7749 1597.55 1776.194
## MtZoa 51 -745.6115 1593.223 1765.125
## MtZoa+I 52 -739.7715 1583.543 1758.816
## MtZoa+G(4) 52 -739.9347 1583.869 1759.143
## MtZoa+G(4)+I 53 -739.7824 1585.565 1764.209
## mtREV24 51 -753.1828 1608.366 1780.268
## mtREV24+I 52 -746.7021 1597.404 1772.677
## mtREV24+G(4) 52 -746.9918 1597.984 1773.257
## mtREV24+G(4)+I 53 -746.8171 1599.634 1778.278
## VT 51 -779.4572 1660.914 1832.817
## VT+I 52 -772.429 1648.858 1824.131
## VT+G(4) 52 -772.932 1649.864 1825.137
## VT+G(4)+I 53 -772.4382 1650.876 1829.52
## RtREV 51 -788.3544 1678.709 1850.611
## RtREV+I 52 -781.0579 1666.116 1841.389
## RtREV+G(4) 52 -781.6547 1667.309 1842.583
## RtREV+G(4)+I 53 -781.066 1668.132 1846.776
## HIVw 51 -818.7671 1739.534 1911.437
## HIVw+I 52 -808.7011 1721.402 1896.675
## HIVw+G(4) 52 -810.1672 1724.334 1899.608
## HIVw+G(4)+I 53 -808.8783 1723.757 1902.4
## HIVb 51 -797.2001 1696.4 1868.303
## HIVb+I 52 -789.0109 1682.022 1857.295
## HIVb+G(4) 52 -789.9841 1683.968 1859.241
## HIVb+G(4)+I 53 -789.1577 1684.315 1862.959
## FLU 51 -794.6883 1691.377 1863.279
## FLU+I 52 -787.7828 1679.566 1854.839
## FLU+G(4) 52 -788.253 1680.506 1855.779
## FLU+G(4)+I 53 -787.8793 1681.759 1860.402
## Blosum62 51 -784.1843 1670.369 1842.271
## Blosum62+I 52 -776.8406 1657.681 1832.954
## Blosum62+G(4) 52 -777.4875 1658.975 1834.248
## Blosum62+G(4)+I 53 -776.8913 1659.783 1838.426
## Dayhoff_DCMut 51 -798.2997 1698.599 1870.502
## Dayhoff_DCMut+I 52 -789.6592 1683.318 1858.592
## Dayhoff_DCMut+G(4) 52 -790.8238 1685.648 1860.921
## Dayhoff_DCMut+G(4)+I 53 -789.817 1685.634 1864.278
## JTT_DCMut 51 -786.2536 1674.507 1846.41
## JTT_DCMut+I 52 -778.2773 1660.555 1835.828
## JTT_DCMut+G(4) 52 -779.1775 1662.355 1837.628
## JTT_DCMut+G(4)+I 53 -778.3787 1662.757 1841.401
Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_1_modeltest, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
mySequences_align_aa_gr_ext_1_modeltest[order(mySequences_align_aa_gr_ext_1_modeltest$AIC), ]
## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -739.7715 1583.543 4.410271e-01 1617.568
## 31 MtZoa+G(4) 52 -739.9347 1583.869 3.745911e-01 1617.894
## 32 MtZoa+G(4)+I 53 -739.7824 1585.565 1.604755e-01 1621.118
## 22 mtmam+I 52 -743.8350 1591.670 7.580609e-03 1625.695
## 23 mtmam+G(4) 52 -743.9617 1591.923 6.678514e-03 1625.948
## 29 MtZoa 51 -745.6115 1593.223 3.487145e-03 1625.763
## 24 mtmam+G(4)+I 53 -743.8491 1593.698 2.749564e-03 1629.251
## 26 mtArt+I 52 -745.7645 1595.529 1.100847e-03 1629.554
## 27 mtArt+G(4) 52 -745.9259 1595.852 9.367109e-04 1629.877
## 34 mtREV24+I 52 -746.7021 1597.404 4.310365e-04 1631.429
## 28 mtArt+G(4)+I 53 -745.7749 1597.550 4.007711e-04 1633.103
## 35 mtREV24+G(4) 52 -746.9918 1597.984 3.226418e-04 1632.008
## 36 mtREV24+G(4)+I 53 -746.8171 1599.634 1.413471e-04 1635.187
## 21 mtmam 51 -749.5626 1601.125 6.707159e-05 1633.665
## 25 mtArt 51 -751.6583 1605.317 8.248022e-06 1637.857
## 33 mtREV24 51 -753.1828 1608.366 1.795847e-06 1640.906
## 18 cpREV+I 52 -768.4012 1640.802 1.624453e-13 1674.827
## 19 cpREV+G(4) 52 -769.3804 1642.761 6.102067e-14 1676.785
## 20 cpREV+G(4)+I 53 -768.4120 1642.824 5.912208e-14 1678.377
## 38 VT+I 52 -772.4290 1648.858 2.893890e-15 1682.883
## 39 VT+G(4) 52 -772.9320 1649.864 1.749909e-15 1683.889
## 40 VT+G(4)+I 53 -772.4382 1650.876 1.054842e-15 1686.429
## 17 cpREV 51 -776.6083 1655.217 1.204272e-16 1687.756
## 58 Blosum62+I 52 -776.8406 1657.681 3.511969e-17 1691.706
## 10 LG+I 52 -777.2918 1658.584 2.236507e-17 1692.608
## 59 Blosum62+G(4) 52 -777.4875 1658.975 1.839098e-17 1693.000
## 6 JTT+I 52 -777.8272 1659.654 1.309358e-17 1693.679
## 60 Blosum62+G(4)+I 53 -776.8913 1659.783 1.228126e-17 1695.335
## 11 LG+G(4) 52 -777.9279 1659.856 1.183988e-17 1693.880
## 66 JTT_DCMut+I 52 -778.2773 1660.555 8.348192e-18 1694.579
## 12 LG+G(4)+I 53 -777.3025 1660.605 8.140374e-18 1696.158
## 37 VT 51 -779.4572 1660.914 6.973852e-18 1693.454
## 7 JTT+G(4) 52 -778.7116 1661.423 5.407067e-18 1695.448
## 8 JTT+G(4)+I 53 -777.9091 1661.818 4.438293e-18 1697.371
## 67 JTT_DCMut+G(4) 52 -779.1775 1662.355 3.393520e-18 1696.380
## 68 JTT_DCMut+G(4)+I 53 -778.3787 1662.757 2.775001e-18 1698.310
## 2 WAG+I 52 -780.0185 1664.037 1.463465e-18 1698.062
## 3 WAG+G(4) 52 -780.9756 1665.951 5.620186e-19 1699.976
## 42 RtREV+I 52 -781.0579 1666.116 5.175693e-19 1700.141
## 4 WAG+G(4)+I 53 -780.1385 1666.277 4.775312e-19 1701.830
## 43 RtREV+G(4) 52 -781.6547 1667.309 2.849806e-19 1701.334
## 44 RtREV+G(4)+I 53 -781.0660 1668.132 1.888820e-19 1703.685
## 57 Blosum62 51 -784.1843 1670.369 6.173369e-20 1702.908
## 9 LG 51 -784.6328 1671.266 3.941927e-20 1703.806
## 5 JTT 51 -785.7615 1673.523 1.275021e-20 1706.063
## 65 JTT_DCMut 51 -786.2536 1674.507 7.795348e-21 1707.047
## 1 WAG 51 -788.1395 1678.279 1.182432e-21 1710.819
## 41 RtREV 51 -788.3544 1678.709 9.537921e-22 1711.249
## 54 FLU+I 52 -787.7828 1679.566 6.214320e-22 1713.590
## 55 FLU+G(4) 52 -788.2530 1680.506 3.883167e-22 1714.531
## 56 FLU+G(4)+I 53 -787.8793 1681.759 2.075831e-22 1717.311
## 50 HIVb+I 52 -789.0109 1682.022 1.819948e-22 1716.046
## 14 Dayhoff+I 52 -789.6021 1683.204 1.007611e-22 1717.229
## 62 Dayhoff_DCMut+I 52 -789.6592 1683.318 9.516454e-23 1717.343
## 51 HIVb+G(4) 52 -789.9841 1683.968 6.876835e-23 1717.993
## 52 HIVb+G(4)+I 53 -789.1577 1684.315 5.780657e-23 1719.868
## 16 Dayhoff+G(4)+I 53 -789.7597 1685.519 3.166325e-23 1721.072
## 15 Dayhoff+G(4) 52 -790.7679 1685.536 3.140474e-23 1719.560
## 64 Dayhoff_DCMut+G(4)+I 53 -789.8170 1685.634 2.989975e-23 1721.187
## 63 Dayhoff_DCMut+G(4) 52 -790.8238 1685.648 2.969622e-23 1719.672
## 53 FLU 51 -794.6883 1691.377 1.693148e-24 1723.916
## 49 HIVb 51 -797.2001 1696.400 1.373472e-25 1728.940
## 13 Dayhoff 51 -798.2470 1698.494 4.821127e-26 1731.034
## 61 Dayhoff_DCMut 51 -798.2997 1698.599 4.573673e-26 1731.139
## 46 HIVw+I 52 -808.7011 1721.402 5.113132e-31 1755.427
## 48 HIVw+G(4)+I 53 -808.8783 1723.757 1.575570e-31 1759.309
## 47 HIVw+G(4) 52 -810.1672 1724.334 1.180213e-31 1758.359
## 45 HIVw 51 -818.7671 1739.534 5.907050e-35 1772.074
## AICcw BIC
## 30 4.812417e-01 1758.816
## 31 4.087478e-01 1759.143
## 32 8.156114e-02 1764.209
## 22 8.271839e-03 1766.943
## 23 7.287488e-03 1767.197
## 29 7.994499e-03 1765.125
## 24 1.397457e-03 1772.342
## 26 1.201227e-03 1770.802
## 27 1.022124e-03 1771.125
## 34 4.703401e-04 1772.677
## 28 2.036905e-04 1776.194
## 35 3.520616e-04 1773.257
## 36 7.183917e-05 1778.278
## 21 1.537658e-04 1773.028
## 25 1.890911e-05 1777.219
## 33 4.117093e-06 1780.268
## 18 1.772577e-13 1816.076
## 19 6.658478e-14 1818.034
## 20 3.004860e-14 1821.468
## 38 3.157767e-15 1824.131
## 39 1.909473e-15 1825.137
## 40 5.361198e-16 1829.520
## 17 2.760869e-16 1827.119
## 58 3.832204e-17 1832.954
## 10 2.440441e-17 1833.857
## 59 2.006795e-17 1834.248
## 6 1.428751e-17 1834.928
## 60 6.241906e-18 1838.426
## 11 1.291949e-17 1835.129
## 66 9.109414e-18 1835.828
## 12 4.137318e-18 1839.249
## 37 1.598799e-17 1832.817
## 7 5.900105e-18 1836.696
## 8 2.255748e-18 1840.462
## 67 3.702955e-18 1837.628
## 68 1.410385e-18 1841.401
## 2 1.596910e-18 1839.310
## 3 6.132657e-19 1841.224
## 42 5.647633e-19 1841.389
## 4 2.427036e-19 1844.921
## 43 3.109663e-19 1842.583
## 44 9.599864e-20 1846.776
## 57 1.415284e-19 1842.271
## 9 9.037116e-20 1843.168
## 5 2.923065e-20 1845.426
## 65 1.787133e-20 1846.410
## 1 2.710800e-21 1850.182
## 41 2.186628e-21 1850.611
## 54 6.780967e-22 1854.839
## 55 4.237250e-22 1855.779
## 56 1.055034e-22 1860.402
## 50 1.985898e-22 1857.295
## 14 1.099490e-22 1858.477
## 62 1.038420e-22 1858.592
## 51 7.503892e-23 1859.241
## 52 2.938000e-23 1862.959
## 16 1.609274e-23 1864.163
## 15 3.426835e-23 1860.809
## 64 1.519645e-23 1864.278
## 63 3.240404e-23 1860.921
## 53 3.881649e-24 1863.279
## 49 3.148771e-25 1868.303
## 13 1.105274e-25 1870.397
## 61 1.048543e-25 1870.502
## 46 5.579368e-31 1896.675
## 48 8.007783e-32 1902.400
## 47 1.287830e-31 1899.608
## 45 1.354228e-34 1911.437
mySequences_align_aa_gr_ext_1_modeltest[order(mySequences_align_aa_gr_ext_1_modeltest$BIC), ]
## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -739.7715 1583.543 4.410271e-01 1617.568
## 31 MtZoa+G(4) 52 -739.9347 1583.869 3.745911e-01 1617.894
## 32 MtZoa+G(4)+I 53 -739.7824 1585.565 1.604755e-01 1621.118
## 29 MtZoa 51 -745.6115 1593.223 3.487145e-03 1625.763
## 22 mtmam+I 52 -743.8350 1591.670 7.580609e-03 1625.695
## 23 mtmam+G(4) 52 -743.9617 1591.923 6.678514e-03 1625.948
## 26 mtArt+I 52 -745.7645 1595.529 1.100847e-03 1629.554
## 27 mtArt+G(4) 52 -745.9259 1595.852 9.367109e-04 1629.877
## 24 mtmam+G(4)+I 53 -743.8491 1593.698 2.749564e-03 1629.251
## 34 mtREV24+I 52 -746.7021 1597.404 4.310365e-04 1631.429
## 21 mtmam 51 -749.5626 1601.125 6.707159e-05 1633.665
## 35 mtREV24+G(4) 52 -746.9918 1597.984 3.226418e-04 1632.008
## 28 mtArt+G(4)+I 53 -745.7749 1597.550 4.007711e-04 1633.103
## 25 mtArt 51 -751.6583 1605.317 8.248022e-06 1637.857
## 36 mtREV24+G(4)+I 53 -746.8171 1599.634 1.413471e-04 1635.187
## 33 mtREV24 51 -753.1828 1608.366 1.795847e-06 1640.906
## 18 cpREV+I 52 -768.4012 1640.802 1.624453e-13 1674.827
## 19 cpREV+G(4) 52 -769.3804 1642.761 6.102067e-14 1676.785
## 20 cpREV+G(4)+I 53 -768.4120 1642.824 5.912208e-14 1678.377
## 38 VT+I 52 -772.4290 1648.858 2.893890e-15 1682.883
## 39 VT+G(4) 52 -772.9320 1649.864 1.749909e-15 1683.889
## 17 cpREV 51 -776.6083 1655.217 1.204272e-16 1687.756
## 40 VT+G(4)+I 53 -772.4382 1650.876 1.054842e-15 1686.429
## 37 VT 51 -779.4572 1660.914 6.973852e-18 1693.454
## 58 Blosum62+I 52 -776.8406 1657.681 3.511969e-17 1691.706
## 10 LG+I 52 -777.2918 1658.584 2.236507e-17 1692.608
## 59 Blosum62+G(4) 52 -777.4875 1658.975 1.839098e-17 1693.000
## 6 JTT+I 52 -777.8272 1659.654 1.309358e-17 1693.679
## 11 LG+G(4) 52 -777.9279 1659.856 1.183988e-17 1693.880
## 66 JTT_DCMut+I 52 -778.2773 1660.555 8.348192e-18 1694.579
## 7 JTT+G(4) 52 -778.7116 1661.423 5.407067e-18 1695.448
## 67 JTT_DCMut+G(4) 52 -779.1775 1662.355 3.393520e-18 1696.380
## 60 Blosum62+G(4)+I 53 -776.8913 1659.783 1.228126e-17 1695.335
## 12 LG+G(4)+I 53 -777.3025 1660.605 8.140374e-18 1696.158
## 2 WAG+I 52 -780.0185 1664.037 1.463465e-18 1698.062
## 8 JTT+G(4)+I 53 -777.9091 1661.818 4.438293e-18 1697.371
## 3 WAG+G(4) 52 -780.9756 1665.951 5.620186e-19 1699.976
## 42 RtREV+I 52 -781.0579 1666.116 5.175693e-19 1700.141
## 68 JTT_DCMut+G(4)+I 53 -778.3787 1662.757 2.775001e-18 1698.310
## 57 Blosum62 51 -784.1843 1670.369 6.173369e-20 1702.908
## 43 RtREV+G(4) 52 -781.6547 1667.309 2.849806e-19 1701.334
## 9 LG 51 -784.6328 1671.266 3.941927e-20 1703.806
## 4 WAG+G(4)+I 53 -780.1385 1666.277 4.775312e-19 1701.830
## 5 JTT 51 -785.7615 1673.523 1.275021e-20 1706.063
## 65 JTT_DCMut 51 -786.2536 1674.507 7.795348e-21 1707.047
## 44 RtREV+G(4)+I 53 -781.0660 1668.132 1.888820e-19 1703.685
## 1 WAG 51 -788.1395 1678.279 1.182432e-21 1710.819
## 41 RtREV 51 -788.3544 1678.709 9.537921e-22 1711.249
## 54 FLU+I 52 -787.7828 1679.566 6.214320e-22 1713.590
## 55 FLU+G(4) 52 -788.2530 1680.506 3.883167e-22 1714.531
## 50 HIVb+I 52 -789.0109 1682.022 1.819948e-22 1716.046
## 14 Dayhoff+I 52 -789.6021 1683.204 1.007611e-22 1717.229
## 62 Dayhoff_DCMut+I 52 -789.6592 1683.318 9.516454e-23 1717.343
## 51 HIVb+G(4) 52 -789.9841 1683.968 6.876835e-23 1717.993
## 56 FLU+G(4)+I 53 -787.8793 1681.759 2.075831e-22 1717.311
## 15 Dayhoff+G(4) 52 -790.7679 1685.536 3.140474e-23 1719.560
## 63 Dayhoff_DCMut+G(4) 52 -790.8238 1685.648 2.969622e-23 1719.672
## 52 HIVb+G(4)+I 53 -789.1577 1684.315 5.780657e-23 1719.868
## 53 FLU 51 -794.6883 1691.377 1.693148e-24 1723.916
## 16 Dayhoff+G(4)+I 53 -789.7597 1685.519 3.166325e-23 1721.072
## 64 Dayhoff_DCMut+G(4)+I 53 -789.8170 1685.634 2.989975e-23 1721.187
## 49 HIVb 51 -797.2001 1696.400 1.373472e-25 1728.940
## 13 Dayhoff 51 -798.2470 1698.494 4.821127e-26 1731.034
## 61 Dayhoff_DCMut 51 -798.2997 1698.599 4.573673e-26 1731.139
## 46 HIVw+I 52 -808.7011 1721.402 5.113132e-31 1755.427
## 47 HIVw+G(4) 52 -810.1672 1724.334 1.180213e-31 1758.359
## 48 HIVw+G(4)+I 53 -808.8783 1723.757 1.575570e-31 1759.309
## 45 HIVw 51 -818.7671 1739.534 5.907050e-35 1772.074
## AICcw BIC
## 30 4.812417e-01 1758.816
## 31 4.087478e-01 1759.143
## 32 8.156114e-02 1764.209
## 29 7.994499e-03 1765.125
## 22 8.271839e-03 1766.943
## 23 7.287488e-03 1767.197
## 26 1.201227e-03 1770.802
## 27 1.022124e-03 1771.125
## 24 1.397457e-03 1772.342
## 34 4.703401e-04 1772.677
## 21 1.537658e-04 1773.028
## 35 3.520616e-04 1773.257
## 28 2.036905e-04 1776.194
## 25 1.890911e-05 1777.219
## 36 7.183917e-05 1778.278
## 33 4.117093e-06 1780.268
## 18 1.772577e-13 1816.076
## 19 6.658478e-14 1818.034
## 20 3.004860e-14 1821.468
## 38 3.157767e-15 1824.131
## 39 1.909473e-15 1825.137
## 17 2.760869e-16 1827.119
## 40 5.361198e-16 1829.520
## 37 1.598799e-17 1832.817
## 58 3.832204e-17 1832.954
## 10 2.440441e-17 1833.857
## 59 2.006795e-17 1834.248
## 6 1.428751e-17 1834.928
## 11 1.291949e-17 1835.129
## 66 9.109414e-18 1835.828
## 7 5.900105e-18 1836.696
## 67 3.702955e-18 1837.628
## 60 6.241906e-18 1838.426
## 12 4.137318e-18 1839.249
## 2 1.596910e-18 1839.310
## 8 2.255748e-18 1840.462
## 3 6.132657e-19 1841.224
## 42 5.647633e-19 1841.389
## 68 1.410385e-18 1841.401
## 57 1.415284e-19 1842.271
## 43 3.109663e-19 1842.583
## 9 9.037116e-20 1843.168
## 4 2.427036e-19 1844.921
## 5 2.923065e-20 1845.426
## 65 1.787133e-20 1846.410
## 44 9.599864e-20 1846.776
## 1 2.710800e-21 1850.182
## 41 2.186628e-21 1850.611
## 54 6.780967e-22 1854.839
## 55 4.237250e-22 1855.779
## 50 1.985898e-22 1857.295
## 14 1.099490e-22 1858.477
## 62 1.038420e-22 1858.592
## 51 7.503892e-23 1859.241
## 56 1.055034e-22 1860.402
## 15 3.426835e-23 1860.809
## 63 3.240404e-23 1860.921
## 52 2.938000e-23 1862.959
## 53 3.881649e-24 1863.279
## 16 1.609274e-23 1864.163
## 64 1.519645e-23 1864.278
## 49 3.148771e-25 1868.303
## 13 1.105274e-25 1870.397
## 61 1.048543e-25 1870.502
## 46 5.579368e-31 1896.675
## 47 1.287830e-31 1899.608
## 48 8.007783e-32 1902.400
## 45 1.354228e-34 1911.437
Meilleur modele : MtZoa+I
env$`MtZoa+I`
## pml(tree = `tree_MtZoa+I`, data = data, model = "MtZoa", inv = 0.778425208675385)
Construction arbres
# Matrice de ditance
dm_aa_gr_ext_1 <- dist.ml(mySequences_align_aa_gr_ext_1_phangorn, model = "MtZoa")
# Construction arbre NJ
treeNJ_aa_gr_ext_1 <- NJ(dm_aa_gr_ext_1)
Integration des parametres
fit_aa_gr_ext_1 = pml(treeNJ_aa_gr_ext_1, data=mySequences_align_aa_gr_ext_1_phangorn)
fitMtZoa_aa_gr_ext_1 <- update(fit_aa_gr_ext_1, model="MtZoa", inv=0.770287356573796)
fitMtZoa_aa_gr_ext_1 <- optim.pml(fitMtZoa_aa_gr_ext_1, model="MtZoa", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_aa_gr_ext_1 = bootstrap.pml(fitMtZoa_aa_gr_ext_1, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitMtZoa_aa_gr_ext_1$tree), bs_aa_gr_ext_1, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Code NCBI: - MN124272.1 Loxodonta africana voucher - KX395909.1 Elephas maximus voucher
Fusionner avec les cetaces
Sequences_groupe_externe_2 <- c(myNewSequences, myExterneSequences[3:4])
Alignement
mySequences_align_gr_ext_2 = AlignSeqs(Sequences_groupe_externe_2, gapOpening = c(-18,-16), gapExtension = c(-2,-1))
## Determining distance matrix based on shared 9-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.12 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.09 secs
##
## Alignment converged - skipping remaining iteration.
Recherche du meilleur modele
mySequences_align_gr_ext_2_ape = as.DNAbin(mySequences_align_gr_ext_2)
mySequences_align_gr_ext_2_phangorn = as.phyDat(mySequences_align_gr_ext_2_ape)
mySequences_gr_ext_2_modelTest = phangorn::modelTest(mySequences_align_gr_ext_2_phangorn)
## Model df logLik AIC BIC
## JC 51 -4245.675 8593.349 8826.249
## JC+I 52 -4015.497 8134.993 8372.46
## JC+G(4) 52 -4022.889 8149.778 8387.245
## JC+G(4)+I 53 -4013.284 8132.569 8374.602
## F81 54 -4204.149 8516.297 8762.897
## F81+I 55 -3963.175 8036.349 8287.516
## F81+G(4) 55 -3968.892 8047.783 8298.95
## F81+G(4)+I 56 -3959.909 8031.819 8287.553
## K80 52 -3922.849 7949.699 8187.166
## K80+I 53 -3631.248 7368.497 7610.53
## K80+G(4) 53 -3637.966 7381.932 7623.966
## K80+G(4)+I 54 -3626.102 7360.203 7606.804
## HKY 55 -3881.378 7872.756 8123.923
## HKY+I 56 -3566.651 7245.302 7501.036
## HKY+G(4) 56 -3577.181 7266.363 7522.096
## HKY+G(4)+I 57 -3561.811 7237.623 7497.923
## TrNe 53 -3887.414 7880.829 8122.862
## TrNe+I 54 -3604.951 7317.903 7564.503
## TrNe+G(4) 54 -3615.672 7339.345 7585.945
## TrNe+G(4)+I 55 -3599.083 7308.166 7559.333
## TrN 56 -3868.4 7848.8 8104.533
## TrN+I 57 -3563.434 7240.868 7501.168
## TrN+G(4) 57 -3574.396 7262.793 7523.093
## TrN+G(4)+I 58 -3558.06 7232.12 7496.987
## TPM1 53 -3920.389 7946.777 8188.811
## TPM1+I 54 -3630.827 7369.653 7616.254
## TPM1+G(4) 54 -3635.943 7379.886 7626.486
## TPM1+G(4)+I 55 -3625.547 7361.095 7612.262
## K81 53 -3920.389 7946.777 8188.811
## K81+I 54 -3630.827 7369.653 7616.254
## K81+G(4) 54 -3635.943 7379.886 7626.486
## K81+G(4)+I 55 -3625.547 7361.095 7612.262
## TPM1u 56 -3879.249 7870.499 8126.233
## TPM1u+I 57 -3566.145 7246.29 7506.59
## TPM1u+G(4) 57 -3575.483 7264.966 7525.267
## TPM1u+G(4)+I 58 -3561.21 7238.42 7503.287
## TPM2 53 -3892.302 7890.604 8132.637
## TPM2+I 54 -3622.367 7352.733 7599.334
## TPM2+G(4) 54 -3624.945 7357.89 7604.49
## TPM2+G(4)+I 55 -3616.247 7342.494 7593.661
## TPM2u 56 -3860.517 7833.035 8088.768
## TPM2u+I 57 -3563.003 7240.007 7500.307
## TPM2u+G(4) 57 -3573.225 7260.449 7520.749
## TPM2u+G(4)+I 58 -3558.259 7232.518 7497.385
## TPM3 53 -3918.368 7942.737 8184.771
## TPM3+I 54 -3626.116 7360.232 7606.832
## TPM3+G(4) 54 -3630.034 7368.069 7614.669
## TPM3+G(4)+I 55 -3620.013 7350.026 7601.193
## TPM3u 56 -3877.71 7867.42 8123.154
## TPM3u+I 57 -3562.403 7238.806 7499.106
## TPM3u+G(4) 57 -3570.967 7255.933 7516.234
## TPM3u+G(4)+I 58 -3557.044 7230.088 7494.955
## TIM1e 54 -3885.013 7878.027 8124.627
## TIM1e+I 55 -3604.512 7319.024 7570.191
## TIM1e+G(4) 55 -3613.842 7337.684 7588.851
## TIM1e+G(4)+I 56 -3598.323 7308.646 7564.38
## TIM1 57 -3866.314 7846.628 8106.928
## TIM1+I 58 -3562.927 7241.855 7506.722
## TIM1+G(4) 58 -3572.755 7261.509 7526.376
## TIM1+G(4)+I 59 -3557.441 7232.883 7502.316
## TIM2e 54 -3856.504 7821.008 8067.609
## TIM2e+I 55 -3592.35 7294.7 7545.867
## TIM2e+G(4) 55 -3601.766 7313.531 7564.698
## TIM2e+G(4)+I 56 -3585.821 7283.643 7539.376
## TIM2 57 -3847.515 7809.03 8069.331
## TIM2+I 58 -3559.395 7234.79 7499.657
## TIM2+G(4) 58 -3570.089 7256.177 7521.044
## TIM2+G(4)+I 59 -3554.056 7226.113 7495.546
## TIM3e 54 -3882.944 7873.889 8120.489
## TIM3e+I 55 -3599.471 7308.941 7560.108
## TIM3e+G(4) 55 -3607.741 7325.482 7576.649
## TIM3e+G(4)+I 56 -3592.206 7296.413 7552.146
## TIM3 57 -3864.724 7843.448 8103.748
## TIM3+I 58 -3559.121 7234.242 7499.109
## TIM3+G(4) 58 -3568.115 7252.231 7517.098
## TIM3+G(4)+I 59 -3553.109 7224.217 7493.651
## TVMe 55 -3886.239 7882.478 8133.645
## TVMe+I 56 -3616.587 7345.174 7600.908
## TVMe+G(4) 56 -3615.948 7343.896 7599.63
## TVMe+G(4)+I 57 -3609.189 7332.379 7592.679
## TVM 58 -3855.352 7826.704 8091.571
## TVM+I 59 -3557.821 7233.642 7503.076
## TVM+G(4) 59 -3566.119 7250.237 7519.671
## TVM+G(4)+I 60 -3552.739 7225.478 7499.479
## SYM 56 -3850.34 7812.68 8068.414
## SYM+I 57 -3585.309 7284.619 7544.919
## SYM+G(4) 57 -3592.824 7299.648 7559.948
## SYM+G(4)+I 58 -3578.076 7272.153 7537.02
## GTR 59 -3842.291 7802.582 8072.016
## GTR+I 60 -3554.136 7228.271 7502.272
## GTR+G(4) 60 -3562.925 7245.851 7519.851
## GTR+G(4)+I 61 -3548.397 7218.794 7497.361
Trouver le meilleur modele
env <- attr(mySequences_gr_ext_2_modelTest, "env")
ls(env=env)
## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"
mySequences_gr_ext_2_modelTest[order(mySequences_gr_ext_2_modelTest$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 61 -3548.397 7218.794 8.736519e-01 7230.449 8.303779e-01
## 76 TIM3+G(4)+I 59 -3553.109 7224.217 5.803466e-02 7235.093 8.144093e-02
## 84 TVM+G(4)+I 60 -3552.739 7225.478 3.089003e-02 7236.740 3.574069e-02
## 68 TIM2+G(4)+I 59 -3554.056 7226.113 2.249549e-02 7236.988 3.156827e-02
## 90 GTR+I 60 -3554.136 7228.271 7.644561e-03 7239.533 8.844987e-03
## 52 TPM3u+G(4)+I 58 -3557.044 7230.088 3.082764e-03 7240.585 5.227777e-03
## 24 TrN+G(4)+I 58 -3558.060 7232.120 1.116052e-03 7242.617 1.892610e-03
## 44 TPM2u+G(4)+I 58 -3558.259 7232.518 9.147047e-04 7243.015 1.551164e-03
## 60 TIM1+G(4)+I 59 -3557.441 7232.883 7.621265e-04 7243.758 1.069504e-03
## 82 TVM+I 59 -3557.821 7233.642 5.212099e-04 7244.518 7.314219e-04
## 74 TIM3+I 58 -3559.121 7234.242 3.862211e-04 7244.739 6.549569e-04
## 66 TIM2+I 58 -3559.395 7234.790 2.936662e-04 7245.287 4.980015e-04
## 16 HKY+G(4)+I 57 -3561.811 7237.623 7.123703e-05 7247.748 1.454527e-04
## 36 TPM1u+G(4)+I 58 -3561.210 7238.420 4.782756e-05 7248.917 8.110636e-05
## 50 TPM3u+I 57 -3562.403 7238.806 3.942134e-05 7248.932 8.049104e-05
## 42 TPM2u+I 57 -3563.003 7240.007 2.162831e-05 7250.132 4.416098e-05
## 22 TrN+I 57 -3563.434 7240.868 1.405997e-05 7250.994 2.870784e-05
## 58 TIM1+I 58 -3562.927 7241.855 8.584212e-06 7252.352 1.455718e-05
## 14 HKY+I 56 -3566.651 7245.302 1.531749e-06 7255.063 3.752049e-06
## 91 GTR+G(4) 60 -3562.925 7245.851 1.164257e-06 7257.112 1.347080e-06
## 34 TPM1u+I 57 -3566.145 7246.290 9.347707e-07 7256.415 1.908628e-06
## 83 TVM+G(4) 59 -3566.119 7250.237 1.298545e-07 7261.113 1.822268e-07
## 75 TIM3+G(4) 58 -3568.115 7252.231 4.793691e-08 7262.727 8.129180e-08
## 51 TPM3u+G(4) 57 -3570.967 7255.933 7.527420e-09 7266.059 1.536959e-08
## 67 TIM2+G(4) 58 -3570.089 7256.177 6.663263e-09 7266.674 1.129962e-08
## 43 TPM2u+G(4) 57 -3573.225 7260.449 7.871177e-10 7270.575 1.607148e-09
## 59 TIM1+G(4) 58 -3572.755 7261.509 4.632645e-10 7272.006 7.856078e-10
## 23 TrN+G(4) 57 -3574.396 7262.793 2.438613e-10 7272.918 4.979194e-10
## 35 TPM1u+G(4) 57 -3575.483 7264.966 8.225174e-11 7275.092 1.679427e-10
## 15 HKY+G(4) 56 -3577.181 7266.363 4.091893e-11 7276.124 1.002317e-10
## 88 SYM+G(4)+I 58 -3578.076 7272.153 2.262426e-12 7282.650 3.836640e-12
## 64 TIM2e+G(4)+I 56 -3585.821 7283.643 7.238146e-15 7293.404 1.772998e-14
## 86 SYM+I 57 -3585.309 7284.619 4.442437e-15 7294.744 9.070630e-15
## 62 TIM2e+I 55 -3592.350 7294.700 2.873928e-17 7304.105 8.414995e-17
## 72 TIM3e+G(4)+I 56 -3592.206 7296.413 1.220756e-17 7306.174 2.990266e-17
## 87 SYM+G(4) 57 -3592.824 7299.648 2.421661e-18 7309.773 4.944581e-18
## 20 TrNe+G(4)+I 55 -3599.083 7308.166 3.423187e-20 7317.571 1.002325e-19
## 56 TIM1e+G(4)+I 56 -3598.323 7308.646 2.692820e-20 7318.407 6.596115e-20
## 70 TIM3e+I 55 -3599.471 7308.941 2.323210e-20 7318.346 6.802468e-20
## 63 TIM2e+G(4) 55 -3601.766 7313.531 2.340967e-21 7322.936 6.854460e-21
## 18 TrNe+I 54 -3604.951 7317.903 2.631265e-22 7326.957 9.176550e-22
## 54 TIM1e+I 55 -3604.512 7319.024 1.501575e-22 7328.429 4.396683e-22
## 71 TIM3e+G(4) 55 -3607.741 7325.482 5.946378e-24 7334.887 1.741127e-23
## 80 TVMe+G(4)+I 57 -3609.189 7332.379 1.890870e-25 7342.505 3.860805e-25
## 55 TIM1e+G(4) 55 -3613.842 7337.684 1.332461e-26 7347.089 3.901509e-26
## 19 TrNe+G(4) 54 -3615.672 7339.345 5.808574e-27 7348.400 2.025743e-26
## 40 TPM2+G(4)+I 55 -3616.247 7342.494 1.202558e-27 7351.899 3.521147e-27
## 79 TVMe+G(4) 56 -3615.948 7343.896 5.966799e-28 7353.658 1.461579e-27
## 78 TVMe+I 56 -3616.587 7345.174 3.149581e-28 7354.935 7.714960e-28
## 48 TPM3+G(4)+I 55 -3620.013 7350.026 2.784179e-29 7359.430 8.152207e-29
## 38 TPM2+I 54 -3622.367 7352.733 7.190944e-30 7361.788 2.507846e-29
## 39 TPM2+G(4) 54 -3624.945 7357.890 5.457204e-31 7366.945 1.903203e-30
## 12 K80+G(4)+I 54 -3626.102 7360.203 1.716521e-31 7369.258 5.986375e-31
## 46 TPM3+I 54 -3626.116 7360.232 1.692037e-31 7369.287 5.900989e-31
## 28 TPM1+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 32 K81+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 47 TPM3+G(4) 54 -3630.034 7368.069 3.362956e-33 7377.124 1.172833e-32
## 10 K80+I 53 -3631.248 7368.497 2.715083e-33 7377.209 1.123781e-32
## 26 TPM1+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 30 K81+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 27 TPM1+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 31 K81+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 11 K80+G(4) 53 -3637.966 7381.932 3.283595e-36 7390.644 1.359090e-35
## 89 GTR 59 -3842.291 7802.582 1.490650e-127 7813.458 2.091852e-127
## 65 TIM2 57 -3847.515 7809.030 5.931339e-129 7819.156 1.211069e-128
## 85 SYM 56 -3850.340 7812.680 9.561794e-130 7822.442 2.342180e-129
## 61 TIM2e 54 -3856.504 7821.008 1.486457e-131 7830.063 5.184027e-131
## 81 TVM 58 -3855.352 7826.704 8.615674e-133 7837.201 1.461053e-132
## 41 TPM2u 56 -3860.517 7833.035 3.635948e-134 7842.796 8.906324e-134
## 73 TIM3 57 -3864.724 7843.448 1.992692e-136 7853.574 4.068706e-136
## 57 TIM1 57 -3866.314 7846.628 4.064257e-137 7856.753 8.298455e-137
## 21 TrN 56 -3868.400 7848.800 1.371896e-137 7858.561 3.360487e-137
## 49 TPM3u 56 -3877.710 7867.420 1.241634e-141 7877.181 3.041407e-141
## 33 TPM1u 56 -3879.249 7870.499 2.663040e-142 7880.260 6.523168e-142
## 13 HKY 55 -3881.378 7872.756 8.615647e-143 7882.161 2.522702e-142
## 69 TIM3e 54 -3882.944 7873.889 4.889345e-143 7882.944 1.705162e-142
## 53 TIM1e 54 -3885.013 7878.027 6.176051e-144 7887.082 2.153901e-143
## 17 TrNe 53 -3887.414 7880.829 1.521693e-144 7889.541 6.298332e-144
## 77 TVMe 55 -3886.239 7882.478 6.669618e-145 7891.883 1.952895e-144
## 37 TPM2 53 -3892.302 7890.604 1.147295e-146 7899.316 4.748687e-146
## 45 TPM3 53 -3918.368 7942.737 5.484169e-158 7951.449 2.269914e-157
## 25 TPM1 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 29 K81 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 9 K80 52 -3922.849 7949.699 1.687822e-159 7958.076 8.261569e-159
## 8 F81+G(4)+I 56 -3959.909 8031.819 2.484339e-177 8041.580 6.085436e-177
## 6 F81+I 55 -3963.175 8036.349 2.578995e-178 8045.754 7.551418e-178
## 7 F81+G(4) 55 -3968.892 8047.783 8.484333e-181 8057.188 2.484252e-180
## 4 JC+G(4)+I 53 -4013.284 8132.569 3.293723e-199 8141.281 1.363282e-198
## 2 JC+I 52 -4015.497 8134.993 9.799726e-200 8143.370 4.796781e-199
## 3 JC+G(4) 52 -4022.889 8149.778 6.034317e-203 8158.155 2.953685e-202
## 5 F81 54 -4204.149 8516.297 1.556283e-282 8525.352 5.427547e-282
## 1 JC 51 -4245.675 8593.349 2.887012e-299 8601.398 1.665264e-298
## BIC
## 92 7497.361
## 76 7493.651
## 84 7499.479
## 68 7495.546
## 90 7502.272
## 52 7494.955
## 24 7496.987
## 44 7497.385
## 60 7502.316
## 82 7503.076
## 74 7499.109
## 66 7499.657
## 16 7497.923
## 36 7503.287
## 50 7499.106
## 42 7500.307
## 22 7501.168
## 58 7506.722
## 14 7501.036
## 91 7519.851
## 34 7506.590
## 83 7519.671
## 75 7517.098
## 51 7516.234
## 67 7521.044
## 43 7520.749
## 59 7526.376
## 23 7523.093
## 35 7525.267
## 15 7522.096
## 88 7537.020
## 64 7539.376
## 86 7544.919
## 62 7545.867
## 72 7552.146
## 87 7559.948
## 20 7559.333
## 56 7564.380
## 70 7560.108
## 63 7564.698
## 18 7564.503
## 54 7570.191
## 71 7576.649
## 80 7592.679
## 55 7588.851
## 19 7585.945
## 40 7593.661
## 79 7599.630
## 78 7600.908
## 48 7601.193
## 38 7599.334
## 39 7604.490
## 12 7606.804
## 46 7606.832
## 28 7612.262
## 32 7612.262
## 47 7614.669
## 10 7610.530
## 26 7616.254
## 30 7616.254
## 27 7626.486
## 31 7626.486
## 11 7623.966
## 89 8072.016
## 65 8069.331
## 85 8068.414
## 61 8067.609
## 81 8091.571
## 41 8088.768
## 73 8103.748
## 57 8106.928
## 21 8104.533
## 49 8123.154
## 33 8126.233
## 13 8123.923
## 69 8120.489
## 53 8124.627
## 17 8122.862
## 77 8133.645
## 37 8132.637
## 45 8184.771
## 25 8188.811
## 29 8188.811
## 9 8187.166
## 8 8287.553
## 6 8287.516
## 7 8298.950
## 4 8374.602
## 2 8372.460
## 3 8387.245
## 5 8762.897
## 1 8826.249
mySequences_gr_ext_2_modelTest[order(mySequences_gr_ext_2_modelTest$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 76 TIM3+G(4)+I 59 -3553.109 7224.217 5.803466e-02 7235.093 8.144093e-02
## 52 TPM3u+G(4)+I 58 -3557.044 7230.088 3.082764e-03 7240.585 5.227777e-03
## 68 TIM2+G(4)+I 59 -3554.056 7226.113 2.249549e-02 7236.988 3.156827e-02
## 24 TrN+G(4)+I 58 -3558.060 7232.120 1.116052e-03 7242.617 1.892610e-03
## 92 GTR+G(4)+I 61 -3548.397 7218.794 8.736519e-01 7230.449 8.303779e-01
## 44 TPM2u+G(4)+I 58 -3558.259 7232.518 9.147047e-04 7243.015 1.551164e-03
## 16 HKY+G(4)+I 57 -3561.811 7237.623 7.123703e-05 7247.748 1.454527e-04
## 50 TPM3u+I 57 -3562.403 7238.806 3.942134e-05 7248.932 8.049104e-05
## 74 TIM3+I 58 -3559.121 7234.242 3.862211e-04 7244.739 6.549569e-04
## 84 TVM+G(4)+I 60 -3552.739 7225.478 3.089003e-02 7236.740 3.574069e-02
## 66 TIM2+I 58 -3559.395 7234.790 2.936662e-04 7245.287 4.980015e-04
## 42 TPM2u+I 57 -3563.003 7240.007 2.162831e-05 7250.132 4.416098e-05
## 14 HKY+I 56 -3566.651 7245.302 1.531749e-06 7255.063 3.752049e-06
## 22 TrN+I 57 -3563.434 7240.868 1.405997e-05 7250.994 2.870784e-05
## 90 GTR+I 60 -3554.136 7228.271 7.644561e-03 7239.533 8.844987e-03
## 60 TIM1+G(4)+I 59 -3557.441 7232.883 7.621265e-04 7243.758 1.069504e-03
## 82 TVM+I 59 -3557.821 7233.642 5.212099e-04 7244.518 7.314219e-04
## 36 TPM1u+G(4)+I 58 -3561.210 7238.420 4.782756e-05 7248.917 8.110636e-05
## 34 TPM1u+I 57 -3566.145 7246.290 9.347707e-07 7256.415 1.908628e-06
## 58 TIM1+I 58 -3562.927 7241.855 8.584212e-06 7252.352 1.455718e-05
## 51 TPM3u+G(4) 57 -3570.967 7255.933 7.527420e-09 7266.059 1.536959e-08
## 75 TIM3+G(4) 58 -3568.115 7252.231 4.793691e-08 7262.727 8.129180e-08
## 83 TVM+G(4) 59 -3566.119 7250.237 1.298545e-07 7261.113 1.822268e-07
## 91 GTR+G(4) 60 -3562.925 7245.851 1.164257e-06 7257.112 1.347080e-06
## 43 TPM2u+G(4) 57 -3573.225 7260.449 7.871177e-10 7270.575 1.607148e-09
## 67 TIM2+G(4) 58 -3570.089 7256.177 6.663263e-09 7266.674 1.129962e-08
## 15 HKY+G(4) 56 -3577.181 7266.363 4.091893e-11 7276.124 1.002317e-10
## 23 TrN+G(4) 57 -3574.396 7262.793 2.438613e-10 7272.918 4.979194e-10
## 35 TPM1u+G(4) 57 -3575.483 7264.966 8.225174e-11 7275.092 1.679427e-10
## 59 TIM1+G(4) 58 -3572.755 7261.509 4.632645e-10 7272.006 7.856078e-10
## 88 SYM+G(4)+I 58 -3578.076 7272.153 2.262426e-12 7282.650 3.836640e-12
## 64 TIM2e+G(4)+I 56 -3585.821 7283.643 7.238146e-15 7293.404 1.772998e-14
## 86 SYM+I 57 -3585.309 7284.619 4.442437e-15 7294.744 9.070630e-15
## 62 TIM2e+I 55 -3592.350 7294.700 2.873928e-17 7304.105 8.414995e-17
## 72 TIM3e+G(4)+I 56 -3592.206 7296.413 1.220756e-17 7306.174 2.990266e-17
## 20 TrNe+G(4)+I 55 -3599.083 7308.166 3.423187e-20 7317.571 1.002325e-19
## 87 SYM+G(4) 57 -3592.824 7299.648 2.421661e-18 7309.773 4.944581e-18
## 70 TIM3e+I 55 -3599.471 7308.941 2.323210e-20 7318.346 6.802468e-20
## 56 TIM1e+G(4)+I 56 -3598.323 7308.646 2.692820e-20 7318.407 6.596115e-20
## 18 TrNe+I 54 -3604.951 7317.903 2.631265e-22 7326.957 9.176550e-22
## 63 TIM2e+G(4) 55 -3601.766 7313.531 2.340967e-21 7322.936 6.854460e-21
## 54 TIM1e+I 55 -3604.512 7319.024 1.501575e-22 7328.429 4.396683e-22
## 71 TIM3e+G(4) 55 -3607.741 7325.482 5.946378e-24 7334.887 1.741127e-23
## 19 TrNe+G(4) 54 -3615.672 7339.345 5.808574e-27 7348.400 2.025743e-26
## 55 TIM1e+G(4) 55 -3613.842 7337.684 1.332461e-26 7347.089 3.901509e-26
## 80 TVMe+G(4)+I 57 -3609.189 7332.379 1.890870e-25 7342.505 3.860805e-25
## 40 TPM2+G(4)+I 55 -3616.247 7342.494 1.202558e-27 7351.899 3.521147e-27
## 38 TPM2+I 54 -3622.367 7352.733 7.190944e-30 7361.788 2.507846e-29
## 79 TVMe+G(4) 56 -3615.948 7343.896 5.966799e-28 7353.658 1.461579e-27
## 78 TVMe+I 56 -3616.587 7345.174 3.149581e-28 7354.935 7.714960e-28
## 48 TPM3+G(4)+I 55 -3620.013 7350.026 2.784179e-29 7359.430 8.152207e-29
## 39 TPM2+G(4) 54 -3624.945 7357.890 5.457204e-31 7366.945 1.903203e-30
## 12 K80+G(4)+I 54 -3626.102 7360.203 1.716521e-31 7369.258 5.986375e-31
## 46 TPM3+I 54 -3626.116 7360.232 1.692037e-31 7369.287 5.900989e-31
## 10 K80+I 53 -3631.248 7368.497 2.715083e-33 7377.209 1.123781e-32
## 28 TPM1+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 32 K81+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 47 TPM3+G(4) 54 -3630.034 7368.069 3.362956e-33 7377.124 1.172833e-32
## 26 TPM1+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 30 K81+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 11 K80+G(4) 53 -3637.966 7381.932 3.283595e-36 7390.644 1.359090e-35
## 27 TPM1+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 31 K81+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 61 TIM2e 54 -3856.504 7821.008 1.486457e-131 7830.063 5.184027e-131
## 85 SYM 56 -3850.340 7812.680 9.561794e-130 7822.442 2.342180e-129
## 65 TIM2 57 -3847.515 7809.030 5.931339e-129 7819.156 1.211069e-128
## 89 GTR 59 -3842.291 7802.582 1.490650e-127 7813.458 2.091852e-127
## 41 TPM2u 56 -3860.517 7833.035 3.635948e-134 7842.796 8.906324e-134
## 81 TVM 58 -3855.352 7826.704 8.615674e-133 7837.201 1.461053e-132
## 73 TIM3 57 -3864.724 7843.448 1.992692e-136 7853.574 4.068706e-136
## 21 TrN 56 -3868.400 7848.800 1.371896e-137 7858.561 3.360487e-137
## 57 TIM1 57 -3866.314 7846.628 4.064257e-137 7856.753 8.298455e-137
## 69 TIM3e 54 -3882.944 7873.889 4.889345e-143 7882.944 1.705162e-142
## 17 TrNe 53 -3887.414 7880.829 1.521693e-144 7889.541 6.298332e-144
## 49 TPM3u 56 -3877.710 7867.420 1.241634e-141 7877.181 3.041407e-141
## 13 HKY 55 -3881.378 7872.756 8.615647e-143 7882.161 2.522702e-142
## 53 TIM1e 54 -3885.013 7878.027 6.176051e-144 7887.082 2.153901e-143
## 33 TPM1u 56 -3879.249 7870.499 2.663040e-142 7880.260 6.523168e-142
## 37 TPM2 53 -3892.302 7890.604 1.147295e-146 7899.316 4.748687e-146
## 77 TVMe 55 -3886.239 7882.478 6.669618e-145 7891.883 1.952895e-144
## 45 TPM3 53 -3918.368 7942.737 5.484169e-158 7951.449 2.269914e-157
## 9 K80 52 -3922.849 7949.699 1.687822e-159 7958.076 8.261569e-159
## 25 TPM1 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 29 K81 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 6 F81+I 55 -3963.175 8036.349 2.578995e-178 8045.754 7.551418e-178
## 8 F81+G(4)+I 56 -3959.909 8031.819 2.484339e-177 8041.580 6.085436e-177
## 7 F81+G(4) 55 -3968.892 8047.783 8.484333e-181 8057.188 2.484252e-180
## 2 JC+I 52 -4015.497 8134.993 9.799726e-200 8143.370 4.796781e-199
## 4 JC+G(4)+I 53 -4013.284 8132.569 3.293723e-199 8141.281 1.363282e-198
## 3 JC+G(4) 52 -4022.889 8149.778 6.034317e-203 8158.155 2.953685e-202
## 5 F81 54 -4204.149 8516.297 1.556283e-282 8525.352 5.427547e-282
## 1 JC 51 -4245.675 8593.349 2.887012e-299 8601.398 1.665264e-298
## BIC
## 76 7493.651
## 52 7494.955
## 68 7495.546
## 24 7496.987
## 92 7497.361
## 44 7497.385
## 16 7497.923
## 50 7499.106
## 74 7499.109
## 84 7499.479
## 66 7499.657
## 42 7500.307
## 14 7501.036
## 22 7501.168
## 90 7502.272
## 60 7502.316
## 82 7503.076
## 36 7503.287
## 34 7506.590
## 58 7506.722
## 51 7516.234
## 75 7517.098
## 83 7519.671
## 91 7519.851
## 43 7520.749
## 67 7521.044
## 15 7522.096
## 23 7523.093
## 35 7525.267
## 59 7526.376
## 88 7537.020
## 64 7539.376
## 86 7544.919
## 62 7545.867
## 72 7552.146
## 20 7559.333
## 87 7559.948
## 70 7560.108
## 56 7564.380
## 18 7564.503
## 63 7564.698
## 54 7570.191
## 71 7576.649
## 19 7585.945
## 55 7588.851
## 80 7592.679
## 40 7593.661
## 38 7599.334
## 79 7599.630
## 78 7600.908
## 48 7601.193
## 39 7604.490
## 12 7606.804
## 46 7606.832
## 10 7610.530
## 28 7612.262
## 32 7612.262
## 47 7614.669
## 26 7616.254
## 30 7616.254
## 11 7623.966
## 27 7626.486
## 31 7626.486
## 61 8067.609
## 85 8068.414
## 65 8069.331
## 89 8072.016
## 41 8088.768
## 81 8091.571
## 73 8103.748
## 21 8104.533
## 57 8106.928
## 69 8120.489
## 17 8122.862
## 49 8123.154
## 13 8123.923
## 53 8124.627
## 33 8126.233
## 37 8132.637
## 77 8133.645
## 45 8184.771
## 9 8187.166
## 25 8188.811
## 29 8188.811
## 6 8287.516
## 8 8287.553
## 7 8298.950
## 2 8372.460
## 4 8374.602
## 3 8387.245
## 5 8762.897
## 1 8826.249
Meilleur modele: TIM3+G(4)+I
env$`TIM3+G(4)+I`
## pml(tree = `tree_TIM3+G(4)+I`, data = data, bf = c(0.269455971803763,
## 0.265704053209027, 0.168154169745893, 0.296685805241317), Q = c(0.217532543290871,
## 10.3742034797635, 1, 0.217532543290871, 15.4906238569354, 1),
## model = "TIM3", inv = 0.578802070346248, k = 4, shape = 3.51925700550295)
Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_2 = dist.logDet(mySequences_align_gr_ext_2_phangorn) # TIM3 existe pas donc utilise dist.logDet
# Construction arbre NJ
treeNJ_gr_ext_2 <- NJ(mySequences_align_gr_ext_2)
# Visualisation
plot(treeNJ_gr_ext_2, main="Arbre NJ Groupe externe 2")
Integration des parametres
fit_gr_ext_2 = pml(treeNJ_gr_ext_2, data=mySequences_align_gr_ext_2_phangorn)
fitTIM3_gr_ext_2 <- update(fit_gr_ext_2, model="TIM3", k=4, inv=0.57880211554897, shape=3.51926023272271)
fitTIM3_gr_ext_2 <- optim.pml(fitTIM3_gr_ext_2, model="TIM3", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_gr_ext_2 = bootstrap.pml(fitTIM3_gr_ext_2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTIM3_gr_ext_2$tree), bs_gr_ext_2, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Alignement
mySequences_align_aa_gr_ext_2 = AlignTranslation(Sequences_groupe_externe_2,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.05 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.05 secs
##
## Alignment converged - skipping remaining iteration.
Conversion
mySequences_align_aa_gr_ext_2_ape = as.AAbin(mySequences_align_aa_gr_ext_2)
mySequences_align_aa_gr_ext_2_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_2_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
Recherche du meilleur modele
mySequences_align_aa_gr_ext_2_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_2_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 51 -882.803 1867.606 2043.39
## WAG+I 52 -873.045 1850.09 2029.32
## WAG+G(4) 52 -873.4912 1850.982 2030.213
## WAG+G(4)+I 53 -873.0976 1852.195 2034.872
## JTT 51 -878.4193 1858.839 2034.622
## JTT+I 52 -868.8141 1841.628 2020.859
## JTT+G(4) 52 -869.2302 1842.46 2021.691
## JTT+G(4)+I 53 -868.842 1843.684 2026.361
## LG 51 -878.6655 1859.331 2035.115
## LG+I 52 -869.9485 1843.897 2023.127
## LG+G(4) 52 -870.1609 1844.322 2023.552
## LG+G(4)+I 53 -870.0532 1846.106 2028.783
## Dayhoff 51 -893.5243 1889.049 2064.832
## Dayhoff+I 52 -882.9789 1869.958 2049.188
## Dayhoff+G(4) 52 -883.5904 1871.181 2050.411
## Dayhoff+G(4)+I 53 -883.0527 1872.105 2054.782
## cpREV 51 -870.6275 1843.255 2019.039
## cpREV+I 52 -860.9882 1825.976 2005.207
## cpREV+G(4) 52 -861.3964 1826.793 2006.023
## cpREV+G(4)+I 53 -861.1584 1828.317 2010.994
## mtmam 51 -838.8119 1779.624 1955.407
## mtmam+I 52 -832.0069 1768.014 1947.244
## mtmam+G(4) 52 -832.0989 1768.198 1947.428
## mtmam+G(4)+I 53 -832.0177 1770.035 1952.712
## mtArt 51 -843.3283 1788.657 1964.44
## mtArt+I 52 -835.9722 1775.944 1955.175
## mtArt+G(4) 52 -836.0526 1776.105 1955.336
## mtArt+G(4)+I 53 -835.9819 1777.964 1960.641
## MtZoa 51 -836.5178 1775.036 1950.819
## MtZoa+I 52 -829.337 1762.674 1941.904
## MtZoa+G(4) 52 -829.4184 1762.837 1942.067
## MtZoa+G(4)+I 53 -829.3528 1764.706 1947.383
## mtREV24 51 -846.478 1794.956 1970.74
## mtREV24+I 52 -838.5859 1781.172 1960.402
## mtREV24+G(4) 52 -838.6387 1781.277 1960.508
## mtREV24+G(4)+I 53 -838.755 1783.51 1966.187
## VT 51 -875.5437 1853.087 2028.871
## VT+I 52 -866.9042 1837.808 2017.039
## VT+G(4) 52 -867.1174 1838.235 2017.465
## VT+G(4)+I 53 -867.0605 1840.121 2022.798
## RtREV 51 -883.3528 1868.706 2044.489
## RtREV+I 52 -874.7996 1853.599 2032.83
## RtREV+G(4) 52 -874.9566 1853.913 2033.144
## RtREV+G(4)+I 53 -874.9087 1855.817 2038.494
## HIVw 51 -912.015 1926.03 2101.814
## HIVw+I 52 -900.3747 1904.749 2083.98
## HIVw+G(4) 52 -901.1 1906.2 2085.43
## HIVw+G(4)+I 53 -900.216 1906.432 2089.109
## HIVb 51 -890.6387 1883.277 2059.061
## HIVb+I 52 -880.5819 1865.164 2044.394
## HIVb+G(4) 52 -881.0801 1866.16 2045.39
## HIVb+G(4)+I 53 -880.6306 1867.261 2049.938
## FLU 51 -884.9149 1871.83 2047.613
## FLU+I 52 -876.2556 1856.511 2035.742
## FLU+G(4) 52 -876.4943 1856.989 2036.219
## FLU+G(4)+I 53 -876.3837 1858.767 2041.444
## Blosum62 51 -880.9273 1863.855 2039.638
## Blosum62+I 52 -872.0477 1848.095 2027.326
## Blosum62+G(4) 52 -872.2876 1848.575 2027.806
## Blosum62+G(4)+I 53 -872.1772 1850.354 2033.031
## Dayhoff_DCMut 51 -893.5996 1889.199 2064.983
## Dayhoff_DCMut+I 52 -883.0602 1870.12 2049.351
## Dayhoff_DCMut+G(4) 52 -883.671 1871.342 2050.572
## Dayhoff_DCMut+G(4)+I 53 -883.135 1872.27 2054.947
## JTT_DCMut 51 -879.0681 1860.136 2035.92
## JTT_DCMut+I 52 -869.4004 1842.801 2022.031
## JTT_DCMut+G(4) 52 -869.8305 1843.661 2022.891
## JTT_DCMut+G(4)+I 53 -869.4308 1844.862 2027.539
Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_2_modeltest, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
mySequences_align_aa_gr_ext_2_modeltest[order(mySequences_align_aa_gr_ext_2_modeltest$AIC), ]
## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -829.3370 1762.674 4.086509e-01 1793.467
## 31 MtZoa+G(4) 52 -829.4184 1762.837 3.767111e-01 1793.630
## 32 MtZoa+G(4)+I 53 -829.3528 1764.706 1.479743e-01 1796.863
## 22 mtmam+I 52 -832.0069 1768.014 2.830140e-02 1798.807
## 23 mtmam+G(4) 52 -832.0989 1768.198 2.581390e-02 1798.991
## 24 mtmam+G(4)+I 53 -832.0177 1770.035 1.030049e-02 1802.193
## 29 MtZoa 51 -836.5178 1775.036 8.454015e-04 1804.502
## 26 mtArt+I 52 -835.9722 1775.944 5.366910e-04 1806.738
## 27 mtArt+G(4) 52 -836.0526 1776.105 4.952221e-04 1806.898
## 28 mtArt+G(4)+I 53 -835.9819 1777.964 1.955327e-04 1810.121
## 21 mtmam 51 -838.8119 1779.624 8.525823e-05 1809.091
## 34 mtREV24+I 52 -838.5859 1781.172 3.931862e-05 1811.965
## 35 mtREV24+G(4) 52 -838.6387 1781.277 3.729804e-05 1812.071
## 36 mtREV24+G(4)+I 53 -838.7550 1783.510 1.221371e-05 1815.667
## 25 mtArt 51 -843.3283 1788.657 9.317811e-07 1818.123
## 33 mtREV24 51 -846.4780 1794.956 3.993832e-08 1824.423
## 18 cpREV+I 52 -860.9882 1825.976 7.335240e-15 1856.770
## 19 cpREV+G(4) 52 -861.3964 1826.793 4.876822e-15 1857.586
## 20 cpREV+G(4)+I 53 -861.1584 1828.317 2.276193e-15 1860.474
## 38 VT+I 52 -866.9042 1837.808 1.977559e-17 1868.602
## 39 VT+G(4) 52 -867.1174 1838.235 1.597761e-17 1869.028
## 40 VT+G(4)+I 53 -867.0605 1840.121 6.221998e-18 1872.278
## 6 JTT+I 52 -868.8141 1841.628 2.928622e-18 1872.421
## 7 JTT+G(4) 52 -869.2302 1842.460 1.931736e-18 1873.254
## 66 JTT_DCMut+I 52 -869.4004 1842.801 1.629502e-18 1873.594
## 17 cpREV 51 -870.6275 1843.255 1.298399e-18 1872.722
## 67 JTT_DCMut+G(4) 52 -869.8305 1843.661 1.059877e-18 1874.454
## 8 JTT+G(4)+I 53 -868.8420 1843.684 1.047731e-18 1875.841
## 10 LG+I 52 -869.9485 1843.897 9.419195e-19 1874.690
## 11 LG+G(4) 52 -870.1609 1844.322 7.616255e-19 1875.115
## 68 JTT_DCMut+G(4)+I 53 -869.4308 1844.862 5.814963e-19 1877.019
## 12 LG+G(4)+I 53 -870.0532 1846.106 3.120693e-19 1878.264
## 58 Blosum62+I 52 -872.0477 1848.095 1.154323e-19 1878.889
## 59 Blosum62+G(4) 52 -872.2876 1848.575 9.080846e-20 1879.369
## 2 WAG+I 52 -873.0450 1850.090 4.257993e-20 1880.883
## 60 Blosum62+G(4)+I 53 -872.1772 1850.354 3.730746e-20 1882.512
## 3 WAG+G(4) 52 -873.4912 1850.982 2.725396e-20 1881.776
## 4 WAG+G(4)+I 53 -873.0976 1852.195 1.486175e-20 1884.352
## 37 VT 51 -875.5437 1853.087 9.513497e-21 1882.554
## 42 RtREV+I 52 -874.7996 1853.599 7.365235e-21 1884.393
## 43 RtREV+G(4) 52 -874.9566 1853.913 6.295037e-21 1884.707
## 44 RtREV+G(4)+I 53 -874.9087 1855.817 2.429545e-21 1887.975
## 54 FLU+I 52 -876.2556 1856.511 1.717291e-21 1887.305
## 55 FLU+G(4) 52 -876.4943 1856.989 1.352725e-21 1887.782
## 56 FLU+G(4)+I 53 -876.3837 1858.767 5.558368e-22 1890.925
## 5 JTT 51 -878.4193 1858.839 5.363792e-22 1888.305
## 9 LG 51 -878.6655 1859.331 4.193163e-22 1888.798
## 65 JTT_DCMut 51 -879.0681 1860.136 2.803550e-22 1889.603
## 57 Blosum62 51 -880.9273 1863.855 4.367880e-23 1893.321
## 50 HIVb+I 52 -880.5819 1865.164 2.269622e-23 1895.957
## 51 HIVb+G(4) 52 -881.0801 1866.160 1.379187e-23 1896.953
## 52 HIVb+G(4)+I 53 -880.6306 1867.261 7.953253e-24 1899.418
## 1 WAG 51 -882.8030 1867.606 6.693393e-24 1897.073
## 41 RtREV 51 -883.3528 1868.706 3.862618e-24 1898.172
## 14 Dayhoff+I 52 -882.9789 1869.958 2.065250e-24 1900.751
## 62 Dayhoff_DCMut+I 52 -883.0602 1870.120 1.903931e-24 1900.914
## 15 Dayhoff+G(4) 52 -883.5904 1871.181 1.120450e-24 1901.974
## 63 Dayhoff_DCMut+G(4) 52 -883.6710 1871.342 1.033650e-24 1902.135
## 53 FLU 51 -884.9149 1871.830 8.099834e-25 1901.296
## 16 Dayhoff+G(4)+I 53 -883.0527 1872.105 7.057312e-25 1904.263
## 64 Dayhoff_DCMut+G(4)+I 53 -883.1350 1872.270 6.499520e-25 1904.427
## 49 HIVb 51 -890.6387 1883.277 2.646449e-27 1912.744
## 13 Dayhoff 51 -893.5243 1889.049 1.477272e-28 1918.515
## 61 Dayhoff_DCMut 51 -893.5996 1889.199 1.370038e-28 1918.666
## 46 HIVw+I 52 -900.3747 1904.749 5.755323e-32 1935.543
## 47 HIVw+G(4) 52 -901.1000 1906.200 2.786460e-32 1936.993
## 48 HIVw+G(4)+I 53 -900.2160 1906.432 2.481503e-32 1938.589
## 45 HIVw 51 -912.0150 1926.030 1.377353e-36 1955.497
## AICcw BIC
## 30 4.429707e-01 1941.904
## 31 4.083485e-01 1942.067
## 32 8.109954e-02 1947.383
## 22 3.067824e-02 1947.244
## 23 2.798184e-02 1947.428
## 24 5.645340e-03 1952.712
## 29 1.778932e-03 1950.819
## 26 5.817640e-04 1955.175
## 27 5.368125e-04 1955.336
## 28 1.071646e-04 1960.641
## 21 1.794043e-04 1955.407
## 34 4.262072e-05 1960.402
## 35 4.043044e-05 1960.508
## 36 6.693906e-06 1966.187
## 25 1.960696e-06 1964.440
## 33 8.404004e-08 1970.740
## 18 7.951277e-15 2005.207
## 19 5.286393e-15 2006.023
## 20 1.247502e-15 2010.994
## 38 2.143641e-17 2017.039
## 39 1.731946e-17 2017.465
## 40 3.410059e-18 2022.798
## 6 3.174577e-18 2020.859
## 7 2.093969e-18 2021.691
## 66 1.766353e-18 2022.031
## 17 2.732151e-18 2019.039
## 67 1.148889e-18 2022.891
## 8 5.742248e-19 2026.361
## 10 1.021025e-18 2023.127
## 11 8.255892e-19 2023.552
## 68 3.186978e-19 2027.539
## 12 1.710343e-19 2028.783
## 58 1.251266e-19 2027.326
## 59 9.843484e-20 2027.806
## 2 4.615592e-20 2029.320
## 60 2.044691e-20 2033.031
## 3 2.954284e-20 2030.213
## 4 8.145204e-21 2034.872
## 37 2.001874e-20 2028.871
## 42 7.983791e-21 2032.830
## 43 6.823714e-21 2033.144
## 44 1.331549e-21 2038.494
## 54 1.861515e-21 2035.742
## 55 1.466331e-21 2036.219
## 56 3.046347e-22 2041.444
## 5 1.128674e-21 2034.622
## 9 8.823446e-22 2035.115
## 65 5.899357e-22 2035.920
## 57 9.191094e-23 2039.638
## 50 2.460232e-23 2044.394
## 51 1.495015e-23 2045.390
## 52 4.358900e-24 2049.938
## 1 1.408454e-23 2043.390
## 41 8.127898e-24 2044.489
## 14 2.238696e-24 2049.188
## 62 2.063829e-24 2049.351
## 15 1.214549e-24 2050.411
## 63 1.120460e-24 2050.572
## 53 1.704404e-24 2047.613
## 16 3.867866e-25 2054.782
## 64 3.562160e-25 2054.947
## 49 5.568779e-27 2059.061
## 13 3.108543e-28 2064.832
## 61 2.882897e-28 2064.983
## 46 6.238673e-32 2083.980
## 47 3.020476e-32 2085.430
## 48 1.360025e-32 2089.109
## 45 2.898289e-36 2101.814
mySequences_align_aa_gr_ext_2_modeltest[order(mySequences_align_aa_gr_ext_2_modeltest$BIC), ]
## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -829.3370 1762.674 4.086509e-01 1793.467
## 31 MtZoa+G(4) 52 -829.4184 1762.837 3.767111e-01 1793.630
## 22 mtmam+I 52 -832.0069 1768.014 2.830140e-02 1798.807
## 32 MtZoa+G(4)+I 53 -829.3528 1764.706 1.479743e-01 1796.863
## 23 mtmam+G(4) 52 -832.0989 1768.198 2.581390e-02 1798.991
## 29 MtZoa 51 -836.5178 1775.036 8.454015e-04 1804.502
## 24 mtmam+G(4)+I 53 -832.0177 1770.035 1.030049e-02 1802.193
## 26 mtArt+I 52 -835.9722 1775.944 5.366910e-04 1806.738
## 27 mtArt+G(4) 52 -836.0526 1776.105 4.952221e-04 1806.898
## 21 mtmam 51 -838.8119 1779.624 8.525823e-05 1809.091
## 34 mtREV24+I 52 -838.5859 1781.172 3.931862e-05 1811.965
## 35 mtREV24+G(4) 52 -838.6387 1781.277 3.729804e-05 1812.071
## 28 mtArt+G(4)+I 53 -835.9819 1777.964 1.955327e-04 1810.121
## 25 mtArt 51 -843.3283 1788.657 9.317811e-07 1818.123
## 36 mtREV24+G(4)+I 53 -838.7550 1783.510 1.221371e-05 1815.667
## 33 mtREV24 51 -846.4780 1794.956 3.993832e-08 1824.423
## 18 cpREV+I 52 -860.9882 1825.976 7.335240e-15 1856.770
## 19 cpREV+G(4) 52 -861.3964 1826.793 4.876822e-15 1857.586
## 20 cpREV+G(4)+I 53 -861.1584 1828.317 2.276193e-15 1860.474
## 38 VT+I 52 -866.9042 1837.808 1.977559e-17 1868.602
## 39 VT+G(4) 52 -867.1174 1838.235 1.597761e-17 1869.028
## 17 cpREV 51 -870.6275 1843.255 1.298399e-18 1872.722
## 6 JTT+I 52 -868.8141 1841.628 2.928622e-18 1872.421
## 7 JTT+G(4) 52 -869.2302 1842.460 1.931736e-18 1873.254
## 66 JTT_DCMut+I 52 -869.4004 1842.801 1.629502e-18 1873.594
## 40 VT+G(4)+I 53 -867.0605 1840.121 6.221998e-18 1872.278
## 67 JTT_DCMut+G(4) 52 -869.8305 1843.661 1.059877e-18 1874.454
## 10 LG+I 52 -869.9485 1843.897 9.419195e-19 1874.690
## 11 LG+G(4) 52 -870.1609 1844.322 7.616255e-19 1875.115
## 8 JTT+G(4)+I 53 -868.8420 1843.684 1.047731e-18 1875.841
## 58 Blosum62+I 52 -872.0477 1848.095 1.154323e-19 1878.889
## 68 JTT_DCMut+G(4)+I 53 -869.4308 1844.862 5.814963e-19 1877.019
## 59 Blosum62+G(4) 52 -872.2876 1848.575 9.080846e-20 1879.369
## 12 LG+G(4)+I 53 -870.0532 1846.106 3.120693e-19 1878.264
## 37 VT 51 -875.5437 1853.087 9.513497e-21 1882.554
## 2 WAG+I 52 -873.0450 1850.090 4.257993e-20 1880.883
## 3 WAG+G(4) 52 -873.4912 1850.982 2.725396e-20 1881.776
## 42 RtREV+I 52 -874.7996 1853.599 7.365235e-21 1884.393
## 60 Blosum62+G(4)+I 53 -872.1772 1850.354 3.730746e-20 1882.512
## 43 RtREV+G(4) 52 -874.9566 1853.913 6.295037e-21 1884.707
## 5 JTT 51 -878.4193 1858.839 5.363792e-22 1888.305
## 4 WAG+G(4)+I 53 -873.0976 1852.195 1.486175e-20 1884.352
## 9 LG 51 -878.6655 1859.331 4.193163e-22 1888.798
## 54 FLU+I 52 -876.2556 1856.511 1.717291e-21 1887.305
## 65 JTT_DCMut 51 -879.0681 1860.136 2.803550e-22 1889.603
## 55 FLU+G(4) 52 -876.4943 1856.989 1.352725e-21 1887.782
## 44 RtREV+G(4)+I 53 -874.9087 1855.817 2.429545e-21 1887.975
## 57 Blosum62 51 -880.9273 1863.855 4.367880e-23 1893.321
## 56 FLU+G(4)+I 53 -876.3837 1858.767 5.558368e-22 1890.925
## 1 WAG 51 -882.8030 1867.606 6.693393e-24 1897.073
## 50 HIVb+I 52 -880.5819 1865.164 2.269622e-23 1895.957
## 41 RtREV 51 -883.3528 1868.706 3.862618e-24 1898.172
## 51 HIVb+G(4) 52 -881.0801 1866.160 1.379187e-23 1896.953
## 53 FLU 51 -884.9149 1871.830 8.099834e-25 1901.296
## 14 Dayhoff+I 52 -882.9789 1869.958 2.065250e-24 1900.751
## 62 Dayhoff_DCMut+I 52 -883.0602 1870.120 1.903931e-24 1900.914
## 52 HIVb+G(4)+I 53 -880.6306 1867.261 7.953253e-24 1899.418
## 15 Dayhoff+G(4) 52 -883.5904 1871.181 1.120450e-24 1901.974
## 63 Dayhoff_DCMut+G(4) 52 -883.6710 1871.342 1.033650e-24 1902.135
## 16 Dayhoff+G(4)+I 53 -883.0527 1872.105 7.057312e-25 1904.263
## 64 Dayhoff_DCMut+G(4)+I 53 -883.1350 1872.270 6.499520e-25 1904.427
## 49 HIVb 51 -890.6387 1883.277 2.646449e-27 1912.744
## 13 Dayhoff 51 -893.5243 1889.049 1.477272e-28 1918.515
## 61 Dayhoff_DCMut 51 -893.5996 1889.199 1.370038e-28 1918.666
## 46 HIVw+I 52 -900.3747 1904.749 5.755323e-32 1935.543
## 47 HIVw+G(4) 52 -901.1000 1906.200 2.786460e-32 1936.993
## 48 HIVw+G(4)+I 53 -900.2160 1906.432 2.481503e-32 1938.589
## 45 HIVw 51 -912.0150 1926.030 1.377353e-36 1955.497
## AICcw BIC
## 30 4.429707e-01 1941.904
## 31 4.083485e-01 1942.067
## 22 3.067824e-02 1947.244
## 32 8.109954e-02 1947.383
## 23 2.798184e-02 1947.428
## 29 1.778932e-03 1950.819
## 24 5.645340e-03 1952.712
## 26 5.817640e-04 1955.175
## 27 5.368125e-04 1955.336
## 21 1.794043e-04 1955.407
## 34 4.262072e-05 1960.402
## 35 4.043044e-05 1960.508
## 28 1.071646e-04 1960.641
## 25 1.960696e-06 1964.440
## 36 6.693906e-06 1966.187
## 33 8.404004e-08 1970.740
## 18 7.951277e-15 2005.207
## 19 5.286393e-15 2006.023
## 20 1.247502e-15 2010.994
## 38 2.143641e-17 2017.039
## 39 1.731946e-17 2017.465
## 17 2.732151e-18 2019.039
## 6 3.174577e-18 2020.859
## 7 2.093969e-18 2021.691
## 66 1.766353e-18 2022.031
## 40 3.410059e-18 2022.798
## 67 1.148889e-18 2022.891
## 10 1.021025e-18 2023.127
## 11 8.255892e-19 2023.552
## 8 5.742248e-19 2026.361
## 58 1.251266e-19 2027.326
## 68 3.186978e-19 2027.539
## 59 9.843484e-20 2027.806
## 12 1.710343e-19 2028.783
## 37 2.001874e-20 2028.871
## 2 4.615592e-20 2029.320
## 3 2.954284e-20 2030.213
## 42 7.983791e-21 2032.830
## 60 2.044691e-20 2033.031
## 43 6.823714e-21 2033.144
## 5 1.128674e-21 2034.622
## 4 8.145204e-21 2034.872
## 9 8.823446e-22 2035.115
## 54 1.861515e-21 2035.742
## 65 5.899357e-22 2035.920
## 55 1.466331e-21 2036.219
## 44 1.331549e-21 2038.494
## 57 9.191094e-23 2039.638
## 56 3.046347e-22 2041.444
## 1 1.408454e-23 2043.390
## 50 2.460232e-23 2044.394
## 41 8.127898e-24 2044.489
## 51 1.495015e-23 2045.390
## 53 1.704404e-24 2047.613
## 14 2.238696e-24 2049.188
## 62 2.063829e-24 2049.351
## 52 4.358900e-24 2049.938
## 15 1.214549e-24 2050.411
## 63 1.120460e-24 2050.572
## 16 3.867866e-25 2054.782
## 64 3.562160e-25 2054.947
## 49 5.568779e-27 2059.061
## 13 3.108543e-28 2064.832
## 61 2.882897e-28 2064.983
## 46 6.238673e-32 2083.980
## 47 3.020476e-32 2085.430
## 48 1.360025e-32 2089.109
## 45 2.898289e-36 2101.814
Meilleur modele : MtZoa+I
env$`MtZoa+I`
## pml(tree = `tree_MtZoa+I`, data = data, model = "MtZoa", inv = 0.733691146551266)
Construction arbres
# Matrice de ditance
dm_aa_gr_ext_2 <- dist.ml(mySequences_align_aa_gr_ext_2_phangorn, model = "MtZoa")
# Construction arbre NJ
treeNJ_aa_gr_ext_2 <- NJ(dm_aa_gr_ext_2)
Integration des parametres
fit_aa_gr_ext_2 = pml(treeNJ_aa_gr_ext_2, data=mySequences_align_aa_gr_ext_2_phangorn)
fitMtZoa_aa_gr_ext_2 <- update(fit_aa_gr_ext_2, model="MtZoa", inv=0.737372323527904)
fitMtZoa_aa_gr_ext_2 <- optim.pml(fitMtZoa_aa_gr_ext_2, model="MtZoa", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_aa_gr_ext_2 = bootstrap.pml(fitMtZoa_aa_gr_ext_2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitMtZoa_aa_gr_ext_2$tree), bs_aa_gr_ext_2, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Code NCBI: - NC_000889.1 Hippopotamus amphibius mitochondrion - NC_020697.1 Hexaprotodon liberiensis isolate
Fusionner avec les cetaces
Sequences_groupe_externe_3 <- c(myNewSequences, myExterneSequences[5:6])
Alignement
mySequences_align_gr_ext_3 = AlignSeqs(Sequences_groupe_externe_3, gapOpening = c(-18,-16), gapExtension = c(-2,-1))
## Determining distance matrix based on shared 11-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.54 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.3 secs
##
## Alignment converged - skipping remaining iteration.
Recherche du meilleur modele
mySequences_align_gr_ext_3_ape = as.DNAbin(mySequences_align_gr_ext_3)
mySequences_align_gr_ext_3_phangorn = as.phyDat(mySequences_align_gr_ext_3_ape)
mySequences_gr_ext_3_modelTest = phangorn::modelTest(mySequences_align_gr_ext_3_phangorn)
## Model df logLik AIC BIC
## JC 51 -30545.14 61192.28 61585.27
## JC+I 52 -30308.99 60721.98 61122.67
## JC+G(4) 52 -30321.38 60746.77 61147.46
## JC+G(4)+I 53 -30308.43 60722.85 61131.25
## F81 54 -29849.89 59807.78 60223.89
## F81+I 55 -29596.55 59303.09 59726.9
## F81+G(4) 55 -29609.53 59329.06 59752.87
## F81+G(4)+I 56 -29596.04 59304.08 59735.6
## K80 52 -29553.92 59211.84 59612.54
## K80+I 53 -29273.48 58652.97 59061.37
## K80+G(4) 53 -29278.31 58662.63 59071.03
## K80+G(4)+I 54 -29268.61 58645.21 59061.32
## HKY 55 -28822.41 57754.82 58178.63
## HKY+I 56 -28488.1 57088.2 57519.72
## HKY+G(4) 56 -28499.12 57110.24 57541.76
## HKY+G(4)+I 57 -28485.21 57084.42 57523.64
## TrNe 53 -29525.37 59156.74 59565.14
## TrNe+I 54 -29251.79 58611.58 59027.68
## TrNe+G(4) 54 -29259.18 58626.36 59042.47
## TrNe+G(4)+I 55 -29247.28 58604.55 59028.36
## TrN 56 -28820.25 57752.49 58184.01
## TrN+I 57 -28488.03 57090.06 57529.28
## TrN+G(4) 57 -28499.11 57112.22 57551.44
## TrN+G(4)+I 58 -28485.19 57086.38 57533.3
## TPM1 53 -29553.92 59213.84 59622.24
## TPM1+I 54 -29273.46 58654.92 59071.03
## TPM1+G(4) 54 -29278.31 58664.62 59080.72
## TPM1+G(4)+I 55 -29268.6 58647.21 59071.02
## K81 53 -29553.92 59213.84 59622.24
## K81+I 54 -29273.46 58654.92 59071.03
## K81+G(4) 54 -29278.31 58664.62 59080.72
## K81+G(4)+I 55 -29268.6 58647.21 59071.02
## TPM1u 56 -28822.4 57756.8 58188.31
## TPM1u+I 57 -28488.08 57090.17 57529.39
## TPM1u+G(4) 57 -28499.07 57112.14 57551.36
## TPM1u+G(4)+I 58 -28485.18 57086.36 57533.29
## TPM2 53 -29530.37 59166.73 59575.13
## TPM2+I 54 -29263.02 58634.04 59050.14
## TPM2+G(4) 54 -29265.82 58639.65 59055.75
## TPM2+G(4)+I 55 -29256.56 58623.13 59046.94
## TPM2u 56 -28813.36 57738.72 58170.23
## TPM2u+I 57 -28486.89 57087.79 57527.01
## TPM2u+G(4) 57 -28497.79 57109.58 57548.8
## TPM2u+G(4)+I 58 -28484.1 57084.21 57531.14
## TPM3 53 -29553.39 59212.79 59621.19
## TPM3+I 54 -29272.2 58652.39 59068.5
## TPM3+G(4) 54 -29276.93 58661.87 59077.97
## TPM3+G(4)+I 55 -29267.19 58644.37 59068.18
## TPM3u 56 -28821.67 57755.34 58186.86
## TPM3u+I 57 -28486.73 57087.45 57526.67
## TPM3u+G(4) 57 -28497.5 57109 57548.22
## TPM3u+G(4)+I 58 -28483.74 57083.48 57530.41
## TIM1e 54 -29525.37 59158.74 59574.85
## TIM1e+I 55 -29251.77 58613.55 59037.36
## TIM1e+G(4) 55 -29259.18 58628.36 59052.17
## TIM1e+G(4)+I 56 -29247.27 58606.54 59038.06
## TIM1 57 -28820.23 57754.47 58193.69
## TIM1+I 58 -28488.01 57092.03 57538.95
## TIM1+G(4) 58 -28499.06 57114.12 57561.04
## TIM1+G(4)+I 59 -28485.16 57088.32 57542.96
## TIM2e 54 -29501.48 59110.95 59527.06
## TIM2e+I 55 -29238.43 58586.86 59010.67
## TIM2e+G(4) 55 -29245.96 58601.92 59025.73
## TIM2e+G(4)+I 56 -29234.19 58580.37 59011.89
## TIM2 57 -28811.16 57736.33 58175.55
## TIM2+I 58 -28486.84 57089.68 57536.61
## TIM2+G(4) 58 -28497.78 57111.57 57558.5
## TIM2+G(4)+I 59 -28484.09 57086.19 57540.82
## TIM3e 54 -29524.84 59157.68 59573.79
## TIM3e+I 55 -29250.44 58610.87 59034.68
## TIM3e+G(4) 55 -29257.81 58625.61 59049.42
## TIM3e+G(4)+I 56 -29245.88 58603.76 59035.28
## TIM3 57 -28819.5 57753.01 58192.23
## TIM3+I 58 -28486.66 57089.31 57536.24
## TIM3+G(4) 58 -28497.49 57110.98 57557.9
## TIM3+G(4)+I 59 -28483.72 57085.45 57540.08
## TVMe 55 -29529.65 59169.3 59593.11
## TVMe+I 56 -29261.4 58634.8 59066.31
## TVMe+G(4) 56 -29264.21 58640.42 59071.93
## TVMe+G(4)+I 57 -29254.95 58623.91 59063.13
## TVM 58 -28812.42 57740.84 58187.77
## TVM+I 59 -28485.21 57088.41 57543.04
## TVM+G(4) 59 -28495.91 57109.82 57564.46
## TVM+G(4)+I 60 -28482.36 57084.71 57547.05
## SYM 56 -29500.76 59113.52 59545.03
## SYM+I 57 -29236.87 58587.73 59026.96
## SYM+G(4) 57 -29244.37 58602.74 59041.97
## SYM+G(4)+I 58 -29232.61 58581.23 59028.16
## GTR 59 -28810.23 57738.45 58193.08
## GTR+I 60 -28485.15 57090.3 57552.64
## GTR+G(4) 60 -28495.91 57111.82 57574.15
## GTR+G(4)+I 61 -28482.35 57086.69 57556.74
Trouver le meilleur modele
env <- attr(mySequences_gr_ext_3_modelTest, "env")
ls(env=env)
## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"
mySequences_gr_ext_3_modelTest[order(mySequences_gr_ext_3_modelTest$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 52 TPM3u+G(4)+I 58 -28483.74 57083.48 2.035756e-01 57083.90 2.040058e-01
## 44 TPM2u+G(4)+I 58 -28484.10 57084.21 1.416496e-01 57084.63 1.419490e-01
## 16 HKY+G(4)+I 57 -28485.21 57084.42 1.277156e-01 57084.82 1.288983e-01
## 84 TVM+G(4)+I 60 -28482.36 57084.71 1.100551e-01 57085.16 1.086910e-01
## 76 TIM3+G(4)+I 59 -28483.72 57085.45 7.633252e-02 57085.88 7.594279e-02
## 68 TIM2+G(4)+I 59 -28484.09 57086.19 5.264087e-02 57086.62 5.237210e-02
## 36 TPM1u+G(4)+I 58 -28485.18 57086.36 4.822142e-02 57086.78 4.832333e-02
## 24 TrN+G(4)+I 58 -28485.19 57086.38 4.795320e-02 57086.79 4.805454e-02
## 92 GTR+G(4)+I 61 -28482.35 57086.69 4.088827e-02 57087.16 4.008069e-02
## 50 TPM3u+I 57 -28486.73 57087.45 2.798709e-02 57087.86 2.824626e-02
## 42 TPM2u+I 57 -28486.89 57087.79 2.369086e-02 57088.19 2.391025e-02
## 14 HKY+I 56 -28488.10 57088.20 1.925343e-02 57088.59 1.956790e-02
## 60 TIM1+G(4)+I 59 -28485.16 57088.32 1.810362e-02 57088.76 1.801119e-02
## 82 TVM+I 59 -28485.21 57088.41 1.733062e-02 57088.84 1.724214e-02
## 74 TIM3+I 58 -28486.66 57089.31 1.103400e-02 57089.73 1.105732e-02
## 66 TIM2+I 58 -28486.84 57089.68 9.193478e-03 57090.10 9.212907e-03
## 22 TrN+I 57 -28488.03 57090.06 7.600912e-03 57090.46 7.671300e-03
## 34 TPM1u+I 57 -28488.08 57090.17 7.203964e-03 57090.57 7.270676e-03
## 90 GTR+I 60 -28485.15 57090.30 6.723302e-03 57090.75 6.639970e-03
## 58 TIM1+I 58 -28488.01 57092.03 2.843981e-03 57092.44 2.849991e-03
## 51 TPM3u+G(4) 57 -28497.50 57109.00 5.857448e-07 57109.41 5.911691e-07
## 43 TPM2u+G(4) 57 -28497.79 57109.58 4.391711e-07 57109.98 4.432380e-07
## 83 TVM+G(4) 59 -28495.91 57109.82 3.880581e-07 57110.26 3.860767e-07
## 15 HKY+G(4) 56 -28499.12 57110.24 3.148417e-07 57110.63 3.199841e-07
## 75 TIM3+G(4) 58 -28497.49 57110.98 2.182222e-07 57111.39 2.186833e-07
## 67 TIM2+G(4) 58 -28497.78 57111.57 1.622141e-07 57111.99 1.625569e-07
## 91 GTR+G(4) 60 -28495.91 57111.82 1.434459e-07 57112.26 1.416680e-07
## 35 TPM1u+G(4) 57 -28499.07 57112.14 1.218570e-07 57112.55 1.229854e-07
## 23 TrN+G(4) 57 -28499.11 57112.22 1.173580e-07 57112.62 1.184447e-07
## 59 TIM1+G(4) 58 -28499.06 57114.12 4.542330e-08 57114.53 4.551929e-08
## 65 TIM2 57 -28811.16 57736.33 3.513226e-143 57736.73 3.545760e-143
## 89 GTR 59 -28810.23 57738.45 1.214640e-143 57738.88 1.208438e-143
## 41 TPM2u 56 -28813.36 57738.72 1.063013e-143 57739.11 1.080376e-143
## 81 TVM 58 -28812.42 57740.84 3.670644e-144 57741.26 3.678401e-144
## 21 TrN 56 -28820.25 57752.49 1.086040e-146 57752.88 1.103779e-146
## 73 TIM3 57 -28819.50 57753.01 8.386723e-147 57753.41 8.464387e-147
## 57 TIM1 57 -28820.23 57754.47 4.037996e-147 57754.87 4.075389e-147
## 13 HKY 55 -28822.41 57754.82 3.384175e-147 57755.20 3.463127e-147
## 49 TPM3u 56 -28821.67 57755.34 2.613147e-147 57755.73 2.655828e-147
## 33 TPM1u 56 -28822.40 57756.80 1.259758e-147 57757.19 1.280334e-147
## 64 TIM2e+G(4)+I 56 -29234.19 58580.37 0.000000e+00 58580.77 0.000000e+00
## 88 SYM+G(4)+I 58 -29232.61 58581.23 0.000000e+00 58581.65 0.000000e+00
## 62 TIM2e+I 55 -29238.43 58586.86 0.000000e+00 58587.24 0.000000e+00
## 86 SYM+I 57 -29236.87 58587.73 0.000000e+00 58588.14 0.000000e+00
## 63 TIM2e+G(4) 55 -29245.96 58601.92 0.000000e+00 58602.30 0.000000e+00
## 87 SYM+G(4) 57 -29244.37 58602.74 0.000000e+00 58603.15 0.000000e+00
## 72 TIM3e+G(4)+I 56 -29245.88 58603.76 0.000000e+00 58604.15 0.000000e+00
## 20 TrNe+G(4)+I 55 -29247.28 58604.55 0.000000e+00 58604.93 0.000000e+00
## 56 TIM1e+G(4)+I 56 -29247.27 58606.54 0.000000e+00 58606.93 0.000000e+00
## 70 TIM3e+I 55 -29250.44 58610.87 0.000000e+00 58611.25 0.000000e+00
## 18 TrNe+I 54 -29251.79 58611.58 0.000000e+00 58611.94 0.000000e+00
## 54 TIM1e+I 55 -29251.77 58613.55 0.000000e+00 58613.92 0.000000e+00
## 40 TPM2+G(4)+I 55 -29256.56 58623.13 0.000000e+00 58623.50 0.000000e+00
## 80 TVMe+G(4)+I 57 -29254.95 58623.91 0.000000e+00 58624.31 0.000000e+00
## 71 TIM3e+G(4) 55 -29257.81 58625.61 0.000000e+00 58625.99 0.000000e+00
## 19 TrNe+G(4) 54 -29259.18 58626.36 0.000000e+00 58626.73 0.000000e+00
## 55 TIM1e+G(4) 55 -29259.18 58628.36 0.000000e+00 58628.73 0.000000e+00
## 38 TPM2+I 54 -29263.02 58634.04 0.000000e+00 58634.40 0.000000e+00
## 78 TVMe+I 56 -29261.40 58634.80 0.000000e+00 58635.19 0.000000e+00
## 39 TPM2+G(4) 54 -29265.82 58639.65 0.000000e+00 58640.01 0.000000e+00
## 79 TVMe+G(4) 56 -29264.21 58640.42 0.000000e+00 58640.81 0.000000e+00
## 48 TPM3+G(4)+I 55 -29267.19 58644.37 0.000000e+00 58644.75 0.000000e+00
## 12 K80+G(4)+I 54 -29268.61 58645.21 0.000000e+00 58645.58 0.000000e+00
## 28 TPM1+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 32 K81+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 46 TPM3+I 54 -29272.20 58652.39 0.000000e+00 58652.76 0.000000e+00
## 10 K80+I 53 -29273.48 58652.97 0.000000e+00 58653.32 0.000000e+00
## 26 TPM1+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 30 K81+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 47 TPM3+G(4) 54 -29276.93 58661.87 0.000000e+00 58662.23 0.000000e+00
## 11 K80+G(4) 53 -29278.31 58662.63 0.000000e+00 58662.98 0.000000e+00
## 27 TPM1+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 31 K81+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 61 TIM2e 54 -29501.48 59110.95 0.000000e+00 59111.31 0.000000e+00
## 85 SYM 56 -29500.76 59113.52 0.000000e+00 59113.91 0.000000e+00
## 17 TrNe 53 -29525.37 59156.74 0.000000e+00 59157.09 0.000000e+00
## 69 TIM3e 54 -29524.84 59157.68 0.000000e+00 59158.05 0.000000e+00
## 53 TIM1e 54 -29525.37 59158.74 0.000000e+00 59159.11 0.000000e+00
## 37 TPM2 53 -29530.37 59166.73 0.000000e+00 59167.08 0.000000e+00
## 77 TVMe 55 -29529.65 59169.30 0.000000e+00 59169.68 0.000000e+00
## 9 K80 52 -29553.92 59211.84 0.000000e+00 59212.18 0.000000e+00
## 45 TPM3 53 -29553.39 59212.79 0.000000e+00 59213.14 0.000000e+00
## 25 TPM1 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 29 K81 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 6 F81+I 55 -29596.55 59303.09 0.000000e+00 59303.47 0.000000e+00
## 8 F81+G(4)+I 56 -29596.04 59304.08 0.000000e+00 59304.47 0.000000e+00
## 7 F81+G(4) 55 -29609.53 59329.06 0.000000e+00 59329.44 0.000000e+00
## 5 F81 54 -29849.89 59807.78 0.000000e+00 59808.15 0.000000e+00
## 2 JC+I 52 -30308.99 60721.98 0.000000e+00 60722.32 0.000000e+00
## 4 JC+G(4)+I 53 -30308.43 60722.85 0.000000e+00 60723.20 0.000000e+00
## 3 JC+G(4) 52 -30321.38 60746.77 0.000000e+00 60747.10 0.000000e+00
## 1 JC 51 -30545.14 61192.28 0.000000e+00 61192.61 0.000000e+00
## BIC
## 52 57530.41
## 44 57531.14
## 16 57523.64
## 84 57547.05
## 76 57540.08
## 68 57540.82
## 36 57533.29
## 24 57533.30
## 92 57556.74
## 50 57526.67
## 42 57527.01
## 14 57519.72
## 60 57542.96
## 82 57543.04
## 74 57536.24
## 66 57536.61
## 22 57529.28
## 34 57529.39
## 90 57552.64
## 58 57538.95
## 51 57548.22
## 43 57548.80
## 83 57564.46
## 15 57541.76
## 75 57557.90
## 67 57558.50
## 91 57574.15
## 35 57551.36
## 23 57551.44
## 59 57561.04
## 65 58175.55
## 89 58193.08
## 41 58170.23
## 81 58187.77
## 21 58184.01
## 73 58192.23
## 57 58193.69
## 13 58178.63
## 49 58186.86
## 33 58188.31
## 64 59011.89
## 88 59028.16
## 62 59010.67
## 86 59026.96
## 63 59025.73
## 87 59041.97
## 72 59035.28
## 20 59028.36
## 56 59038.06
## 70 59034.68
## 18 59027.68
## 54 59037.36
## 40 59046.94
## 80 59063.13
## 71 59049.42
## 19 59042.47
## 55 59052.17
## 38 59050.14
## 78 59066.31
## 39 59055.75
## 79 59071.93
## 48 59068.18
## 12 59061.32
## 28 59071.02
## 32 59071.02
## 46 59068.50
## 10 59061.37
## 26 59071.03
## 30 59071.03
## 47 59077.97
## 11 59071.03
## 27 59080.72
## 31 59080.72
## 61 59527.06
## 85 59545.03
## 17 59565.14
## 69 59573.79
## 53 59574.85
## 37 59575.13
## 77 59593.11
## 9 59612.54
## 45 59621.19
## 25 59622.24
## 29 59622.24
## 6 59726.90
## 8 59735.60
## 7 59752.87
## 5 60223.89
## 2 61122.67
## 4 61131.25
## 3 61147.46
## 1 61585.27
mySequences_gr_ext_3_modelTest[order(mySequences_gr_ext_3_modelTest$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 14 HKY+I 56 -28488.10 57088.20 1.925343e-02 57088.59 1.956790e-02
## 16 HKY+G(4)+I 57 -28485.21 57084.42 1.277156e-01 57084.82 1.288983e-01
## 50 TPM3u+I 57 -28486.73 57087.45 2.798709e-02 57087.86 2.824626e-02
## 42 TPM2u+I 57 -28486.89 57087.79 2.369086e-02 57088.19 2.391025e-02
## 22 TrN+I 57 -28488.03 57090.06 7.600912e-03 57090.46 7.671300e-03
## 34 TPM1u+I 57 -28488.08 57090.17 7.203964e-03 57090.57 7.270676e-03
## 52 TPM3u+G(4)+I 58 -28483.74 57083.48 2.035756e-01 57083.90 2.040058e-01
## 44 TPM2u+G(4)+I 58 -28484.10 57084.21 1.416496e-01 57084.63 1.419490e-01
## 36 TPM1u+G(4)+I 58 -28485.18 57086.36 4.822142e-02 57086.78 4.832333e-02
## 24 TrN+G(4)+I 58 -28485.19 57086.38 4.795320e-02 57086.79 4.805454e-02
## 74 TIM3+I 58 -28486.66 57089.31 1.103400e-02 57089.73 1.105732e-02
## 66 TIM2+I 58 -28486.84 57089.68 9.193478e-03 57090.10 9.212907e-03
## 58 TIM1+I 58 -28488.01 57092.03 2.843981e-03 57092.44 2.849991e-03
## 76 TIM3+G(4)+I 59 -28483.72 57085.45 7.633252e-02 57085.88 7.594279e-02
## 68 TIM2+G(4)+I 59 -28484.09 57086.19 5.264087e-02 57086.62 5.237210e-02
## 15 HKY+G(4) 56 -28499.12 57110.24 3.148417e-07 57110.63 3.199841e-07
## 60 TIM1+G(4)+I 59 -28485.16 57088.32 1.810362e-02 57088.76 1.801119e-02
## 82 TVM+I 59 -28485.21 57088.41 1.733062e-02 57088.84 1.724214e-02
## 84 TVM+G(4)+I 60 -28482.36 57084.71 1.100551e-01 57085.16 1.086910e-01
## 51 TPM3u+G(4) 57 -28497.50 57109.00 5.857448e-07 57109.41 5.911691e-07
## 43 TPM2u+G(4) 57 -28497.79 57109.58 4.391711e-07 57109.98 4.432380e-07
## 35 TPM1u+G(4) 57 -28499.07 57112.14 1.218570e-07 57112.55 1.229854e-07
## 23 TrN+G(4) 57 -28499.11 57112.22 1.173580e-07 57112.62 1.184447e-07
## 90 GTR+I 60 -28485.15 57090.30 6.723302e-03 57090.75 6.639970e-03
## 92 GTR+G(4)+I 61 -28482.35 57086.69 4.088827e-02 57087.16 4.008069e-02
## 75 TIM3+G(4) 58 -28497.49 57110.98 2.182222e-07 57111.39 2.186833e-07
## 67 TIM2+G(4) 58 -28497.78 57111.57 1.622141e-07 57111.99 1.625569e-07
## 59 TIM1+G(4) 58 -28499.06 57114.12 4.542330e-08 57114.53 4.551929e-08
## 83 TVM+G(4) 59 -28495.91 57109.82 3.880581e-07 57110.26 3.860767e-07
## 91 GTR+G(4) 60 -28495.91 57111.82 1.434459e-07 57112.26 1.416680e-07
## 41 TPM2u 56 -28813.36 57738.72 1.063013e-143 57739.11 1.080376e-143
## 65 TIM2 57 -28811.16 57736.33 3.513226e-143 57736.73 3.545760e-143
## 13 HKY 55 -28822.41 57754.82 3.384175e-147 57755.20 3.463127e-147
## 21 TrN 56 -28820.25 57752.49 1.086040e-146 57752.88 1.103779e-146
## 49 TPM3u 56 -28821.67 57755.34 2.613147e-147 57755.73 2.655828e-147
## 81 TVM 58 -28812.42 57740.84 3.670644e-144 57741.26 3.678401e-144
## 33 TPM1u 56 -28822.40 57756.80 1.259758e-147 57757.19 1.280334e-147
## 73 TIM3 57 -28819.50 57753.01 8.386723e-147 57753.41 8.464387e-147
## 89 GTR 59 -28810.23 57738.45 1.214640e-143 57738.88 1.208438e-143
## 57 TIM1 57 -28820.23 57754.47 4.037996e-147 57754.87 4.075389e-147
## 62 TIM2e+I 55 -29238.43 58586.86 0.000000e+00 58587.24 0.000000e+00
## 64 TIM2e+G(4)+I 56 -29234.19 58580.37 0.000000e+00 58580.77 0.000000e+00
## 63 TIM2e+G(4) 55 -29245.96 58601.92 0.000000e+00 58602.30 0.000000e+00
## 86 SYM+I 57 -29236.87 58587.73 0.000000e+00 58588.14 0.000000e+00
## 18 TrNe+I 54 -29251.79 58611.58 0.000000e+00 58611.94 0.000000e+00
## 88 SYM+G(4)+I 58 -29232.61 58581.23 0.000000e+00 58581.65 0.000000e+00
## 20 TrNe+G(4)+I 55 -29247.28 58604.55 0.000000e+00 58604.93 0.000000e+00
## 70 TIM3e+I 55 -29250.44 58610.87 0.000000e+00 58611.25 0.000000e+00
## 72 TIM3e+G(4)+I 56 -29245.88 58603.76 0.000000e+00 58604.15 0.000000e+00
## 54 TIM1e+I 55 -29251.77 58613.55 0.000000e+00 58613.92 0.000000e+00
## 56 TIM1e+G(4)+I 56 -29247.27 58606.54 0.000000e+00 58606.93 0.000000e+00
## 87 SYM+G(4) 57 -29244.37 58602.74 0.000000e+00 58603.15 0.000000e+00
## 19 TrNe+G(4) 54 -29259.18 58626.36 0.000000e+00 58626.73 0.000000e+00
## 40 TPM2+G(4)+I 55 -29256.56 58623.13 0.000000e+00 58623.50 0.000000e+00
## 71 TIM3e+G(4) 55 -29257.81 58625.61 0.000000e+00 58625.99 0.000000e+00
## 38 TPM2+I 54 -29263.02 58634.04 0.000000e+00 58634.40 0.000000e+00
## 55 TIM1e+G(4) 55 -29259.18 58628.36 0.000000e+00 58628.73 0.000000e+00
## 39 TPM2+G(4) 54 -29265.82 58639.65 0.000000e+00 58640.01 0.000000e+00
## 12 K80+G(4)+I 54 -29268.61 58645.21 0.000000e+00 58645.58 0.000000e+00
## 10 K80+I 53 -29273.48 58652.97 0.000000e+00 58653.32 0.000000e+00
## 80 TVMe+G(4)+I 57 -29254.95 58623.91 0.000000e+00 58624.31 0.000000e+00
## 78 TVMe+I 56 -29261.40 58634.80 0.000000e+00 58635.19 0.000000e+00
## 48 TPM3+G(4)+I 55 -29267.19 58644.37 0.000000e+00 58644.75 0.000000e+00
## 46 TPM3+I 54 -29272.20 58652.39 0.000000e+00 58652.76 0.000000e+00
## 28 TPM1+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 32 K81+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 26 TPM1+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 30 K81+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 11 K80+G(4) 53 -29278.31 58662.63 0.000000e+00 58662.98 0.000000e+00
## 79 TVMe+G(4) 56 -29264.21 58640.42 0.000000e+00 58640.81 0.000000e+00
## 47 TPM3+G(4) 54 -29276.93 58661.87 0.000000e+00 58662.23 0.000000e+00
## 27 TPM1+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 31 K81+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 61 TIM2e 54 -29501.48 59110.95 0.000000e+00 59111.31 0.000000e+00
## 85 SYM 56 -29500.76 59113.52 0.000000e+00 59113.91 0.000000e+00
## 17 TrNe 53 -29525.37 59156.74 0.000000e+00 59157.09 0.000000e+00
## 69 TIM3e 54 -29524.84 59157.68 0.000000e+00 59158.05 0.000000e+00
## 53 TIM1e 54 -29525.37 59158.74 0.000000e+00 59159.11 0.000000e+00
## 37 TPM2 53 -29530.37 59166.73 0.000000e+00 59167.08 0.000000e+00
## 77 TVMe 55 -29529.65 59169.30 0.000000e+00 59169.68 0.000000e+00
## 9 K80 52 -29553.92 59211.84 0.000000e+00 59212.18 0.000000e+00
## 45 TPM3 53 -29553.39 59212.79 0.000000e+00 59213.14 0.000000e+00
## 25 TPM1 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 29 K81 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 6 F81+I 55 -29596.55 59303.09 0.000000e+00 59303.47 0.000000e+00
## 8 F81+G(4)+I 56 -29596.04 59304.08 0.000000e+00 59304.47 0.000000e+00
## 7 F81+G(4) 55 -29609.53 59329.06 0.000000e+00 59329.44 0.000000e+00
## 5 F81 54 -29849.89 59807.78 0.000000e+00 59808.15 0.000000e+00
## 2 JC+I 52 -30308.99 60721.98 0.000000e+00 60722.32 0.000000e+00
## 4 JC+G(4)+I 53 -30308.43 60722.85 0.000000e+00 60723.20 0.000000e+00
## 3 JC+G(4) 52 -30321.38 60746.77 0.000000e+00 60747.10 0.000000e+00
## 1 JC 51 -30545.14 61192.28 0.000000e+00 61192.61 0.000000e+00
## BIC
## 14 57519.72
## 16 57523.64
## 50 57526.67
## 42 57527.01
## 22 57529.28
## 34 57529.39
## 52 57530.41
## 44 57531.14
## 36 57533.29
## 24 57533.30
## 74 57536.24
## 66 57536.61
## 58 57538.95
## 76 57540.08
## 68 57540.82
## 15 57541.76
## 60 57542.96
## 82 57543.04
## 84 57547.05
## 51 57548.22
## 43 57548.80
## 35 57551.36
## 23 57551.44
## 90 57552.64
## 92 57556.74
## 75 57557.90
## 67 57558.50
## 59 57561.04
## 83 57564.46
## 91 57574.15
## 41 58170.23
## 65 58175.55
## 13 58178.63
## 21 58184.01
## 49 58186.86
## 81 58187.77
## 33 58188.31
## 73 58192.23
## 89 58193.08
## 57 58193.69
## 62 59010.67
## 64 59011.89
## 63 59025.73
## 86 59026.96
## 18 59027.68
## 88 59028.16
## 20 59028.36
## 70 59034.68
## 72 59035.28
## 54 59037.36
## 56 59038.06
## 87 59041.97
## 19 59042.47
## 40 59046.94
## 71 59049.42
## 38 59050.14
## 55 59052.17
## 39 59055.75
## 12 59061.32
## 10 59061.37
## 80 59063.13
## 78 59066.31
## 48 59068.18
## 46 59068.50
## 28 59071.02
## 32 59071.02
## 26 59071.03
## 30 59071.03
## 11 59071.03
## 79 59071.93
## 47 59077.97
## 27 59080.72
## 31 59080.72
## 61 59527.06
## 85 59545.03
## 17 59565.14
## 69 59573.79
## 53 59574.85
## 37 59575.13
## 77 59593.11
## 9 59612.54
## 45 59621.19
## 25 59622.24
## 29 59622.24
## 6 59726.90
## 8 59735.60
## 7 59752.87
## 5 60223.89
## 2 61122.67
## 4 61131.25
## 3 61147.46
## 1 61585.27
Meilleur modele: HKY+G(4)+I
env$`HKY+G(4)+I`
## pml(tree = `tree_HKY+G(4)+I`, data = data, bf = c(0.308803455371514,
## 0.278915306725343, 0.148686918077542, 0.263594319825602), Q = c(1,
## 23.8237170745377, 1, 1, 23.8237170745377, 1), model = "HKY",
## inv = 0.616439563626882, k = 4, shape = 5.42291970567487)
Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_3 = dist.logDet(mySequences_align_gr_ext_3_phangorn) #HKY n'existe pas avec dist.ml()
# Construction arbre NJ
treeNJ_gr_ext_3 <- NJ(mySequences_align_gr_ext_3)
# Visualisation
plot(treeNJ_gr_ext_3, main="Arbre NJ Groupe externe 3")
Integration des parametres
fit_gr_ext_3 = pml(treeNJ_gr_ext_3, data=mySequences_align_gr_ext_3_phangorn)
fitHKY_gr_ext_3 <- update(fit_gr_ext_3, model="HKY", k=4, inv=0.616461296091301, shape=5.44888877718601)
fitHKY_gr_ext_3 <- optim.pml(fitHKY_gr_ext_3, model="HKY", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_gr_ext_3 = bootstrap.pml(fitHKY_gr_ext_3, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitHKY_gr_ext_3$tree), bs_gr_ext_3, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Alignement
mySequences_align_aa_gr_ext_3 = AlignTranslation(Sequences_groupe_externe_3,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 6-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 1.14 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.12 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 1.84 secs
Conversion
mySequences_align_aa_gr_ext_3_ape = as.AAbin(mySequences_align_aa_gr_ext_3)
mySequences_align_aa_gr_ext_3_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_3_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
Recherche du meilleur modele
mySequences_align_aa_gr_ext_3_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_3_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 51 -29557.62 59217.25 59571.94
## WAG+I 52 -29532.69 59169.38 59531.03
## WAG+G(4) 52 -29531.57 59167.14 59528.79
## WAG+G(4)+I 53 -29531.59 59169.18 59537.78
## JTT 51 -29442.65 58987.29 59341.98
## JTT+I 52 -29394.5 58893 59254.65
## JTT+G(4) 52 -29391.4 58886.8 59248.44
## JTT+G(4)+I 53 -29391.42 58888.84 59257.44
## LG 51 -29595.62 59293.24 59647.93
## LG+I 52 -29541.89 59187.79 59549.43
## LG+G(4) 52 -29534.56 59173.12 59534.76
## LG+G(4)+I 53 -29534.56 59175.13 59543.72
## Dayhoff 51 -30190.24 60482.49 60837.18
## Dayhoff+I 52 -30193.98 60491.95 60853.59
## Dayhoff+G(4) 52 -30194.67 60493.34 60854.99
## Dayhoff+G(4)+I 53 -30194.7 60495.4 60864
## cpREV 51 -29668.46 59438.91 59793.6
## cpREV+I 52 -29594.14 59292.28 59653.92
## cpREV+G(4) 52 -29594.87 59293.74 59655.39
## cpREV+G(4)+I 53 -29594.39 59294.78 59663.38
## mtmam 51 -30540.11 61182.22 61536.91
## mtmam+I 52 -30511.75 61127.5 61489.14
## mtmam+G(4) 52 -30514.09 61132.19 61493.83
## mtmam+G(4)+I 53 -30513.66 61133.32 61501.92
## mtArt 51 -29807.58 59717.15 60071.84
## mtArt+I 52 -29630.49 59364.98 59726.63
## mtArt+G(4) 52 -29587.87 59279.75 59641.39
## mtArt+G(4)+I 53 -29588.33 59282.67 59651.27
## MtZoa 51 -29742.34 59586.69 59941.38
## MtZoa+I 52 -29608.94 59321.88 59683.52
## MtZoa+G(4) 52 -29584 59272 59633.65
## MtZoa+G(4)+I 53 -29584.28 59274.56 59643.16
## mtREV24 51 -29258.64 58619.28 58973.97
## mtREV24+I 52 -29158.26 58420.51 58782.16
## mtREV24+G(4) 52 -29129 58362 58723.64
## mtREV24+G(4)+I 53 -29129.66 58365.32 58733.91
## VT 51 -29672.99 59447.98 59802.67
## VT+I 52 -29615.27 59334.54 59696.18
## VT+G(4) 52 -29595.31 59294.61 59656.26
## VT+G(4)+I 53 -29595.39 59296.79 59665.39
## RtREV 51 -29379.09 58860.18 59214.86
## RtREV+I 52 -29336.78 58777.56 59139.2
## RtREV+G(4) 52 -29331.3 58766.6 59128.24
## RtREV+G(4)+I 53 -29331.3 58768.61 59137.21
## HIVw 51 -30257.49 60616.98 60971.67
## HIVw+I 52 -30074.73 60253.45 60615.1
## HIVw+G(4) 52 -30052.63 60209.27 60570.91
## HIVw+G(4)+I 53 -30053.48 60212.96 60581.56
## HIVb 51 -29831.46 59764.91 60119.6
## HIVb+I 52 -29705.99 59515.97 59877.62
## HIVb+G(4) 52 -29701.24 59506.48 59868.12
## HIVb+G(4)+I 53 -29700.18 59506.37 59874.97
## FLU 51 -29409.51 58921.03 59275.71
## FLU+I 52 -29320.46 58744.93 59106.57
## FLU+G(4) 52 -30098.84 60301.69 60663.33
## FLU+G(4)+I 53 -30082.19 60270.38 60638.98
## Blosum62 51 -29596.14 59294.28 59648.97
## Blosum62+I 52 -29594.3 59292.61 59654.25
## Blosum62+G(4) 52 -29593.96 59291.92 59653.57
## Blosum62+G(4)+I 53 -29594 59294 59662.6
## Dayhoff_DCMut 51 -30186.65 60475.29 60829.98
## Dayhoff_DCMut+I 52 -30190.37 60484.74 60846.38
## Dayhoff_DCMut+G(4) 52 -30191.08 60486.15 60847.79
## Dayhoff_DCMut+G(4)+I 53 -30191.1 60488.21 60856.8
## JTT_DCMut 51 -29459.26 59020.52 59375.21
## JTT_DCMut+I 52 -29411.19 58926.38 59288.02
## JTT_DCMut+G(4) 52 -29408.31 58920.62 59282.26
## JTT_DCMut+G(4)+I 53 -29408.33 58922.65 59291.25
Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_3_modeltest, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
mySequences_align_aa_gr_ext_3_modeltest[order(mySequences_align_aa_gr_ext_3_modeltest$AIC), ]
## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 52 -29129.00 58362.00 8.399080e-01 58362.72
## 36 mtREV24+G(4)+I 53 -29129.66 58365.32 1.600920e-01 58366.06
## 34 mtREV24+I 52 -29158.26 58420.51 1.654092e-13 58421.23
## 33 mtREV24 51 -29258.64 58619.28 1.139219e-56 58619.97
## 54 FLU+I 52 -29320.46 58744.93 5.925674e-84 58745.64
## 43 RtREV+G(4) 52 -29331.30 58766.60 1.167828e-88 58767.31
## 44 RtREV+G(4)+I 53 -29331.30 58768.61 4.270285e-89 58769.35
## 42 RtREV+I 52 -29336.78 58777.56 4.870374e-91 58778.27
## 41 RtREV 51 -29379.09 58860.18 5.581857e-109 58860.87
## 7 JTT+G(4) 52 -29391.40 58886.80 9.232021e-115 58887.52
## 8 JTT+G(4)+I 53 -29391.42 58888.84 3.334116e-115 58889.58
## 6 JTT+I 52 -29394.50 58893.00 4.152386e-116 58893.72
## 67 JTT_DCMut+G(4) 52 -29408.31 58920.62 4.187962e-122 58921.33
## 53 FLU 51 -29409.51 58921.03 3.415374e-122 58921.72
## 68 JTT_DCMut+G(4)+I 53 -29408.33 58922.65 1.512854e-122 58923.40
## 66 JTT_DCMut+I 52 -29411.19 58926.38 2.351608e-123 58927.09
## 5 JTT 51 -29442.65 58987.29 1.393959e-136 58987.98
## 65 JTT_DCMut 51 -29459.26 59020.52 8.472846e-144 59021.21
## 3 WAG+G(4) 52 -29531.57 59167.14 1.229597e-175 59167.86
## 4 WAG+G(4)+I 53 -29531.59 59169.18 4.436784e-176 59169.93
## 2 WAG+I 52 -29532.69 59169.38 4.008239e-176 59170.10
## 11 LG+G(4) 52 -29534.56 59173.12 6.187572e-177 59173.84
## 12 LG+G(4)+I 53 -29534.56 59175.13 2.272476e-177 59175.87
## 10 LG+I 52 -29541.89 59187.79 4.042479e-180 59188.51
## 1 WAG 51 -29557.62 59217.25 1.620749e-186 59217.94
## 31 MtZoa+G(4) 52 -29584.00 59272.00 2.088449e-198 59272.72
## 32 MtZoa+G(4)+I 53 -29584.28 59274.56 5.816963e-199 59275.30
## 27 mtArt+G(4) 52 -29587.87 59279.75 4.342329e-200 59280.47
## 28 mtArt+G(4)+I 53 -29588.33 59282.67 1.008501e-200 59283.41
## 59 Blosum62+G(4) 52 -29593.96 59291.92 9.868953e-203 59292.64
## 18 cpREV+I 52 -29594.14 59292.28 8.258313e-203 59293.00
## 58 Blosum62+I 52 -29594.30 59292.61 7.001220e-203 59293.33
## 9 LG 51 -29595.62 59293.24 5.109175e-203 59293.93
## 19 cpREV+G(4) 52 -29594.87 59293.74 3.967863e-203 59294.46
## 60 Blosum62+G(4)+I 53 -29594.00 59294.00 3.494117e-203 59294.74
## 57 Blosum62 51 -29596.14 59294.28 3.040701e-203 59294.97
## 39 VT+G(4) 52 -29595.31 59294.61 2.569882e-203 59295.33
## 20 cpREV+G(4)+I 53 -29594.39 59294.78 2.363334e-203 59295.53
## 40 VT+G(4)+I 53 -29595.39 59296.79 8.662865e-204 59297.53
## 30 MtZoa+I 52 -29608.94 59321.88 3.084856e-209 59322.60
## 38 VT+I 52 -29615.27 59334.54 5.501452e-212 59335.25
## 26 mtArt+I 52 -29630.49 59364.98 1.345919e-218 59365.70
## 17 cpREV 51 -29668.46 59438.91 1.190441e-234 59439.60
## 37 VT 51 -29672.99 59447.98 1.278323e-236 59448.67
## 52 HIVb+G(4)+I 53 -29700.18 59506.37 2.678299e-249 59507.11
## 51 HIVb+G(4) 52 -29701.24 59506.48 2.533576e-249 59507.20
## 50 HIVb+I 52 -29705.99 59515.97 2.199549e-251 59516.69
## 29 MtZoa 51 -29742.34 59586.69 9.690624e-267 59587.38
## 25 mtArt 51 -29807.58 59717.15 4.538413e-295 59717.84
## 49 HIVb 51 -29831.46 59764.91 1.930450e-305 59765.60
## 47 HIVw+G(4) 52 -30052.63 60209.27 0.000000e+00 60209.99
## 48 HIVw+G(4)+I 53 -30053.48 60212.96 0.000000e+00 60213.71
## 46 HIVw+I 52 -30074.73 60253.45 0.000000e+00 60254.17
## 56 FLU+G(4)+I 53 -30082.19 60270.38 0.000000e+00 60271.12
## 55 FLU+G(4) 52 -30098.84 60301.69 0.000000e+00 60302.40
## 61 Dayhoff_DCMut 51 -30186.65 60475.29 0.000000e+00 60475.98
## 13 Dayhoff 51 -30190.24 60482.49 0.000000e+00 60483.18
## 62 Dayhoff_DCMut+I 52 -30190.37 60484.74 0.000000e+00 60485.45
## 63 Dayhoff_DCMut+G(4) 52 -30191.08 60486.15 0.000000e+00 60486.87
## 64 Dayhoff_DCMut+G(4)+I 53 -30191.10 60488.21 0.000000e+00 60488.95
## 14 Dayhoff+I 52 -30193.98 60491.95 0.000000e+00 60492.67
## 15 Dayhoff+G(4) 52 -30194.67 60493.34 0.000000e+00 60494.06
## 16 Dayhoff+G(4)+I 53 -30194.70 60495.40 0.000000e+00 60496.14
## 45 HIVw 51 -30257.49 60616.98 0.000000e+00 60617.67
## 22 mtmam+I 52 -30511.75 61127.50 0.000000e+00 61128.21
## 23 mtmam+G(4) 52 -30514.09 61132.19 0.000000e+00 61132.91
## 24 mtmam+G(4)+I 53 -30513.66 61133.32 0.000000e+00 61134.07
## 21 mtmam 51 -30540.11 61182.22 0.000000e+00 61182.91
## AICcw BIC
## 35 8.417590e-01 58723.64
## 36 1.582410e-01 58733.91
## 34 1.657737e-13 58782.16
## 33 1.157325e-56 58973.97
## 54 5.938732e-84 59106.57
## 43 1.170401e-88 59128.24
## 44 4.220911e-89 59137.21
## 42 4.881107e-91 59139.20
## 41 5.670572e-109 59214.86
## 7 9.252366e-115 59248.44
## 8 3.295567e-115 59257.44
## 6 4.161537e-116 59254.65
## 67 4.197191e-122 59282.26
## 53 3.469656e-122 59275.71
## 68 1.495362e-122 59291.25
## 66 2.356790e-123 59288.02
## 5 1.416114e-136 59341.98
## 65 8.607509e-144 59375.21
## 3 1.232307e-175 59528.79
## 4 4.385486e-176 59537.78
## 2 4.017072e-176 59531.03
## 11 6.201208e-177 59534.76
## 12 2.246201e-177 59543.72
## 10 4.051388e-180 59549.43
## 1 1.646509e-186 59571.94
## 31 2.093052e-198 59633.65
## 32 5.749707e-199 59643.16
## 27 4.351899e-200 59641.39
## 28 9.968407e-201 59651.27
## 59 9.890702e-203 59653.57
## 18 8.276513e-203 59653.92
## 58 7.016649e-203 59654.25
## 9 5.190378e-203 59647.93
## 19 3.976607e-203 59655.39
## 60 3.453718e-203 59662.60
## 57 3.089028e-203 59648.97
## 39 2.575546e-203 59656.26
## 20 2.336009e-203 59663.38
## 40 8.562705e-204 59665.39
## 30 3.091654e-209 59683.52
## 38 5.513576e-212 59696.18
## 26 1.348886e-218 59726.63
## 17 1.209361e-234 59793.60
## 37 1.298640e-236 59802.67
## 52 2.647332e-249 59874.97
## 51 2.539159e-249 59868.12
## 50 2.204396e-251 59877.62
## 29 9.844642e-267 59941.38
## 25 4.610544e-295 60071.84
## 49 1.961131e-305 60119.60
## 47 0.000000e+00 60570.91
## 48 0.000000e+00 60581.56
## 46 0.000000e+00 60615.10
## 56 0.000000e+00 60638.98
## 55 0.000000e+00 60663.33
## 61 0.000000e+00 60829.98
## 13 0.000000e+00 60837.18
## 62 0.000000e+00 60846.38
## 63 0.000000e+00 60847.79
## 64 0.000000e+00 60856.80
## 14 0.000000e+00 60853.59
## 15 0.000000e+00 60854.99
## 16 0.000000e+00 60864.00
## 45 0.000000e+00 60971.67
## 22 0.000000e+00 61489.14
## 23 0.000000e+00 61493.83
## 24 0.000000e+00 61501.92
## 21 0.000000e+00 61536.91
mySequences_align_aa_gr_ext_3_modeltest[order(mySequences_align_aa_gr_ext_3_modeltest$BIC), ]
## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 52 -29129.00 58362.00 8.399080e-01 58362.72
## 36 mtREV24+G(4)+I 53 -29129.66 58365.32 1.600920e-01 58366.06
## 34 mtREV24+I 52 -29158.26 58420.51 1.654092e-13 58421.23
## 33 mtREV24 51 -29258.64 58619.28 1.139219e-56 58619.97
## 54 FLU+I 52 -29320.46 58744.93 5.925674e-84 58745.64
## 43 RtREV+G(4) 52 -29331.30 58766.60 1.167828e-88 58767.31
## 44 RtREV+G(4)+I 53 -29331.30 58768.61 4.270285e-89 58769.35
## 42 RtREV+I 52 -29336.78 58777.56 4.870374e-91 58778.27
## 41 RtREV 51 -29379.09 58860.18 5.581857e-109 58860.87
## 7 JTT+G(4) 52 -29391.40 58886.80 9.232021e-115 58887.52
## 6 JTT+I 52 -29394.50 58893.00 4.152386e-116 58893.72
## 8 JTT+G(4)+I 53 -29391.42 58888.84 3.334116e-115 58889.58
## 53 FLU 51 -29409.51 58921.03 3.415374e-122 58921.72
## 67 JTT_DCMut+G(4) 52 -29408.31 58920.62 4.187962e-122 58921.33
## 66 JTT_DCMut+I 52 -29411.19 58926.38 2.351608e-123 58927.09
## 68 JTT_DCMut+G(4)+I 53 -29408.33 58922.65 1.512854e-122 58923.40
## 5 JTT 51 -29442.65 58987.29 1.393959e-136 58987.98
## 65 JTT_DCMut 51 -29459.26 59020.52 8.472846e-144 59021.21
## 3 WAG+G(4) 52 -29531.57 59167.14 1.229597e-175 59167.86
## 2 WAG+I 52 -29532.69 59169.38 4.008239e-176 59170.10
## 11 LG+G(4) 52 -29534.56 59173.12 6.187572e-177 59173.84
## 4 WAG+G(4)+I 53 -29531.59 59169.18 4.436784e-176 59169.93
## 12 LG+G(4)+I 53 -29534.56 59175.13 2.272476e-177 59175.87
## 10 LG+I 52 -29541.89 59187.79 4.042479e-180 59188.51
## 1 WAG 51 -29557.62 59217.25 1.620749e-186 59217.94
## 31 MtZoa+G(4) 52 -29584.00 59272.00 2.088449e-198 59272.72
## 27 mtArt+G(4) 52 -29587.87 59279.75 4.342329e-200 59280.47
## 32 MtZoa+G(4)+I 53 -29584.28 59274.56 5.816963e-199 59275.30
## 9 LG 51 -29595.62 59293.24 5.109175e-203 59293.93
## 57 Blosum62 51 -29596.14 59294.28 3.040701e-203 59294.97
## 28 mtArt+G(4)+I 53 -29588.33 59282.67 1.008501e-200 59283.41
## 59 Blosum62+G(4) 52 -29593.96 59291.92 9.868953e-203 59292.64
## 18 cpREV+I 52 -29594.14 59292.28 8.258313e-203 59293.00
## 58 Blosum62+I 52 -29594.30 59292.61 7.001220e-203 59293.33
## 19 cpREV+G(4) 52 -29594.87 59293.74 3.967863e-203 59294.46
## 39 VT+G(4) 52 -29595.31 59294.61 2.569882e-203 59295.33
## 60 Blosum62+G(4)+I 53 -29594.00 59294.00 3.494117e-203 59294.74
## 20 cpREV+G(4)+I 53 -29594.39 59294.78 2.363334e-203 59295.53
## 40 VT+G(4)+I 53 -29595.39 59296.79 8.662865e-204 59297.53
## 30 MtZoa+I 52 -29608.94 59321.88 3.084856e-209 59322.60
## 38 VT+I 52 -29615.27 59334.54 5.501452e-212 59335.25
## 26 mtArt+I 52 -29630.49 59364.98 1.345919e-218 59365.70
## 17 cpREV 51 -29668.46 59438.91 1.190441e-234 59439.60
## 37 VT 51 -29672.99 59447.98 1.278323e-236 59448.67
## 51 HIVb+G(4) 52 -29701.24 59506.48 2.533576e-249 59507.20
## 52 HIVb+G(4)+I 53 -29700.18 59506.37 2.678299e-249 59507.11
## 50 HIVb+I 52 -29705.99 59515.97 2.199549e-251 59516.69
## 29 MtZoa 51 -29742.34 59586.69 9.690624e-267 59587.38
## 25 mtArt 51 -29807.58 59717.15 4.538413e-295 59717.84
## 49 HIVb 51 -29831.46 59764.91 1.930450e-305 59765.60
## 47 HIVw+G(4) 52 -30052.63 60209.27 0.000000e+00 60209.99
## 48 HIVw+G(4)+I 53 -30053.48 60212.96 0.000000e+00 60213.71
## 46 HIVw+I 52 -30074.73 60253.45 0.000000e+00 60254.17
## 56 FLU+G(4)+I 53 -30082.19 60270.38 0.000000e+00 60271.12
## 55 FLU+G(4) 52 -30098.84 60301.69 0.000000e+00 60302.40
## 61 Dayhoff_DCMut 51 -30186.65 60475.29 0.000000e+00 60475.98
## 13 Dayhoff 51 -30190.24 60482.49 0.000000e+00 60483.18
## 62 Dayhoff_DCMut+I 52 -30190.37 60484.74 0.000000e+00 60485.45
## 63 Dayhoff_DCMut+G(4) 52 -30191.08 60486.15 0.000000e+00 60486.87
## 14 Dayhoff+I 52 -30193.98 60491.95 0.000000e+00 60492.67
## 15 Dayhoff+G(4) 52 -30194.67 60493.34 0.000000e+00 60494.06
## 64 Dayhoff_DCMut+G(4)+I 53 -30191.10 60488.21 0.000000e+00 60488.95
## 16 Dayhoff+G(4)+I 53 -30194.70 60495.40 0.000000e+00 60496.14
## 45 HIVw 51 -30257.49 60616.98 0.000000e+00 60617.67
## 22 mtmam+I 52 -30511.75 61127.50 0.000000e+00 61128.21
## 23 mtmam+G(4) 52 -30514.09 61132.19 0.000000e+00 61132.91
## 24 mtmam+G(4)+I 53 -30513.66 61133.32 0.000000e+00 61134.07
## 21 mtmam 51 -30540.11 61182.22 0.000000e+00 61182.91
## AICcw BIC
## 35 8.417590e-01 58723.64
## 36 1.582410e-01 58733.91
## 34 1.657737e-13 58782.16
## 33 1.157325e-56 58973.97
## 54 5.938732e-84 59106.57
## 43 1.170401e-88 59128.24
## 44 4.220911e-89 59137.21
## 42 4.881107e-91 59139.20
## 41 5.670572e-109 59214.86
## 7 9.252366e-115 59248.44
## 6 4.161537e-116 59254.65
## 8 3.295567e-115 59257.44
## 53 3.469656e-122 59275.71
## 67 4.197191e-122 59282.26
## 66 2.356790e-123 59288.02
## 68 1.495362e-122 59291.25
## 5 1.416114e-136 59341.98
## 65 8.607509e-144 59375.21
## 3 1.232307e-175 59528.79
## 2 4.017072e-176 59531.03
## 11 6.201208e-177 59534.76
## 4 4.385486e-176 59537.78
## 12 2.246201e-177 59543.72
## 10 4.051388e-180 59549.43
## 1 1.646509e-186 59571.94
## 31 2.093052e-198 59633.65
## 27 4.351899e-200 59641.39
## 32 5.749707e-199 59643.16
## 9 5.190378e-203 59647.93
## 57 3.089028e-203 59648.97
## 28 9.968407e-201 59651.27
## 59 9.890702e-203 59653.57
## 18 8.276513e-203 59653.92
## 58 7.016649e-203 59654.25
## 19 3.976607e-203 59655.39
## 39 2.575546e-203 59656.26
## 60 3.453718e-203 59662.60
## 20 2.336009e-203 59663.38
## 40 8.562705e-204 59665.39
## 30 3.091654e-209 59683.52
## 38 5.513576e-212 59696.18
## 26 1.348886e-218 59726.63
## 17 1.209361e-234 59793.60
## 37 1.298640e-236 59802.67
## 51 2.539159e-249 59868.12
## 52 2.647332e-249 59874.97
## 50 2.204396e-251 59877.62
## 29 9.844642e-267 59941.38
## 25 4.610544e-295 60071.84
## 49 1.961131e-305 60119.60
## 47 0.000000e+00 60570.91
## 48 0.000000e+00 60581.56
## 46 0.000000e+00 60615.10
## 56 0.000000e+00 60638.98
## 55 0.000000e+00 60663.33
## 61 0.000000e+00 60829.98
## 13 0.000000e+00 60837.18
## 62 0.000000e+00 60846.38
## 63 0.000000e+00 60847.79
## 14 0.000000e+00 60853.59
## 15 0.000000e+00 60854.99
## 64 0.000000e+00 60856.80
## 16 0.000000e+00 60864.00
## 45 0.000000e+00 60971.67
## 22 0.000000e+00 61489.14
## 23 0.000000e+00 61493.83
## 24 0.000000e+00 61501.92
## 21 0.000000e+00 61536.91
Meilleur modele : mtREV24+G(4)
env$`mtREV24+G(4)`
## pml(tree = `tree_mtREV24+G(4)`, data = data, model = "mtREV24",
## k = 4, shape = 0.568028964692472)
Construction arbres
# Matrice de ditance
dm_aa_gr_ext_3 <- dist.ml(mySequences_align_aa_gr_ext_3_phangorn, model = "mtREV24")
# Construction arbre NJ
treeNJ_aa_gr_ext_3 <- NJ(dm_aa_gr_ext_3)
Integration des parametres
fit_aa_gr_ext_3 = pml(treeNJ_aa_gr_ext_3, data=mySequences_align_aa_gr_ext_3_phangorn)
fitmtREV24_aa_gr_ext_3 <- update(fit_aa_gr_ext_3, model="mtREV24", shape =0.567580580902988, k = 4)
fitmtREV24_aa_gr_ext_3 <- optim.pml(fitmtREV24_aa_gr_ext_3, model="mtREV24", optGamma = TRUE, optShape = TRUE, rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_aa_gr_ext_3 = bootstrap.pml(fitmtREV24_aa_gr_ext_3, multicore=FALSE, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitmtREV24_aa_gr_ext_3$tree), bs_aa_gr_ext_3, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Code NCBI: - GQ152876.1 Dermochelys coriacea voucher - MW478028.1 Emys orbicularis voucher
Fusionner avec les cetaces
Sequences_groupe_externe_4 <- c(myNewSequences, myExterneSequences[7:8])
Alignement
mySequences_align_gr_ext_4 = AlignSeqs(Sequences_groupe_externe_4, gapOpening = c(-18,-16), gapExtension = c(-2,-1))
## Determining distance matrix based on shared 9-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Alignment converged - skipping remaining iteration.
Recherche du meilleur modele
mySequences_align_gr_ext_4_ape = as.DNAbin(mySequences_align_gr_ext_4)
mySequences_align_gr_ext_4_phangorn = as.phyDat(mySequences_align_gr_ext_4_ape)
mySequences_gr_ext_4_modelTest = phangorn::modelTest(mySequences_align_gr_ext_4_phangorn)
## Model df logLik AIC BIC
## JC 51 -4553.439 9208.877 9448.74
## JC+I 52 -4287.999 8679.998 8924.564
## JC+G(4) 52 -4291.647 8687.293 8931.859
## JC+G(4)+I 53 -4284.782 8675.565 8924.834
## F81 54 -4506.634 9121.268 9375.241
## F81+I 55 -4228.498 8566.996 8825.672
## F81+G(4) 55 -4230.284 8570.567 8829.243
## F81+G(4)+I 56 -4224.101 8560.203 8823.581
## K80 52 -4232.278 8568.555 8813.121
## K80+I 53 -3913.845 7933.691 8182.96
## K80+G(4) 53 -3907.147 7920.293 8169.562
## K80+G(4)+I 54 -3904.257 7916.514 8170.487
## HKY 55 -4183.735 8477.47 8736.146
## HKY+I 56 -3839.72 7791.44 8054.819
## HKY+G(4) 56 -3838.137 7788.274 8051.653
## HKY+G(4)+I 57 -3831.107 7776.215 8044.296
## TrNe 53 -4186.79 8479.579 8728.848
## TrNe+I 54 -3880.283 7868.566 8122.539
## TrNe+G(4) 54 -3881.555 7871.11 8125.083
## TrNe+G(4)+I 55 -3869.676 7849.352 8108.028
## TrN 56 -4164.857 8441.714 8705.093
## TrN+I 57 -3835.551 7785.102 8053.183
## TrN+G(4) 57 -3834.876 7783.753 8051.834
## TrN+G(4)+I 58 -3825.467 7766.934 8039.719
## TPM1 53 -4231.337 8568.674 8817.943
## TPM1+I 54 -3913.507 7935.014 8188.986
## TPM1+G(4) 54 -3906.704 7921.407 8175.38
## TPM1+G(4)+I 55 -3903.769 7917.538 8176.214
## K81 53 -4231.337 8568.674 8817.943
## K81+I 54 -3913.507 7935.014 8188.986
## K81+G(4) 54 -3906.704 7921.407 8175.38
## K81+G(4)+I 55 -3903.769 7917.538 8176.214
## TPM1u 56 -4183.048 8478.095 8741.474
## TPM1u+I 57 -3839.307 7792.613 8060.695
## TPM1u+G(4) 57 -3837.719 7789.439 8057.52
## TPM1u+G(4)+I 58 -3830.649 7777.297 8050.082
## TPM2 53 -4195.47 8496.94 8746.209
## TPM2+I 54 -3903.139 7914.278 8168.25
## TPM2+G(4) 54 -3895.221 7898.443 8152.415
## TPM2+G(4)+I 55 -3891.884 7893.767 8152.442
## TPM2u 56 -4158.175 8428.351 8691.729
## TPM2u+I 57 -3835.564 7785.128 8053.209
## TPM2u+G(4) 57 -3835.239 7784.479 8052.56
## TPM2u+G(4)+I 58 -3827.669 7771.338 8044.123
## TPM3 53 -4230.129 8566.257 8815.526
## TPM3+I 54 -3910.077 7928.153 8182.125
## TPM3+G(4) 54 -3902.727 7913.454 8167.426
## TPM3+G(4)+I 55 -3899.63 7909.261 8167.936
## TPM3u 56 -4182.147 8476.295 8739.673
## TPM3u+I 57 -3836.594 7787.187 8055.269
## TPM3u+G(4) 57 -3834.434 7782.869 8050.95
## TPM3u+G(4)+I 58 -3827.543 7771.087 8043.872
## TIM1e 54 -4185.808 8479.616 8733.589
## TIM1e+I 55 -3879.892 7869.783 8128.459
## TIM1e+G(4) 55 -3881.074 7872.148 8130.824
## TIM1e+G(4)+I 56 -3869.253 7850.507 8113.885
## TIM1 57 -4164.146 8442.291 8710.373
## TIM1+I 58 -3835.136 7786.272 8059.057
## TIM1+G(4) 58 -3834.458 7784.916 8057.701
## TIM1+G(4)+I 59 -3825.034 7768.067 8045.555
## TIM2e 54 -4149.681 8407.361 8661.334
## TIM2e+I 55 -3861.02 7832.041 8090.716
## TIM2e+G(4) 55 -3865.431 7840.861 8099.537
## TIM2e+G(4)+I 56 -3852.888 7817.775 8081.154
## TIM2 57 -4139.239 8392.478 8660.56
## TIM2+I 58 -3830.708 7777.417 8050.202
## TIM2+G(4) 58 -3831.158 7778.316 8051.101
## TIM2+G(4)+I 59 -3821.085 7760.169 8037.657
## TIM3e 54 -4184.626 8477.253 8731.225
## TIM3e+I 55 -3875.762 7861.524 8120.199
## TIM3e+G(4) 55 -3876.958 7863.916 8122.592
## TIM3e+G(4)+I 56 -3864.922 7841.845 8105.223
## TIM3 57 -4163.254 8440.508 8708.589
## TIM3+I 58 -3832.285 7780.571 8053.356
## TIM3+G(4) 58 -3831.138 7778.275 8051.06
## TIM3+G(4)+I 59 -3821.76 7761.52 8039.008
## TVMe 55 -4192.004 8494.008 8752.684
## TVMe+I 56 -3898.607 7909.215 8172.593
## TVMe+G(4) 56 -3889.857 7891.714 8155.092
## TVMe+G(4)+I 57 -3886.409 7886.818 8154.899
## TVM 58 -4155.419 8426.837 8699.622
## TVM+I 59 -3831.448 7780.897 8058.385
## TVM+G(4) 59 -3830.532 7779.063 8056.551
## TVM+G(4)+I 60 -3823.18 7766.36 8048.552
## SYM 56 -4146.395 8404.79 8668.169
## SYM+I 57 -3855.407 7824.813 8092.895
## SYM+G(4) 57 -3859.748 7833.496 8101.578
## SYM+G(4)+I 58 -3847.215 7810.431 8083.216
## GTR 59 -4136.615 8391.231 8668.719
## GTR+I 60 -3826.372 7772.745 8054.936
## GTR+G(4) 60 -3826.352 7772.704 8054.896
## GTR+G(4)+I 61 -3816.43 7754.86 8041.754
Trouver le meilleur modele
env <- attr(mySequences_gr_ext_4_modelTest, "env")
ls(env=env)
## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"
mySequences_gr_ext_4_modelTest[order(mySequences_gr_ext_4_modelTest$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 61 -3816.430 7754.860 8.977207e-01 7764.905 8.627364e-01
## 68 TIM2+G(4)+I 59 -3821.085 7760.169 6.312408e-02 7769.547 8.470607e-02
## 76 TIM3+G(4)+I 59 -3821.760 7761.520 3.212413e-02 7770.898 4.310730e-02
## 84 TVM+G(4)+I 60 -3823.180 7766.360 2.856606e-03 7776.068 3.249007e-03
## 24 TrN+G(4)+I 58 -3825.467 7766.934 2.144103e-03 7775.987 3.384116e-03
## 60 TIM1+G(4)+I 59 -3825.034 7768.067 1.216734e-03 7777.445 1.632733e-03
## 52 TPM3u+G(4)+I 58 -3827.543 7771.087 2.688408e-04 7780.140 4.243213e-04
## 44 TPM2u+G(4)+I 58 -3827.669 7771.338 2.370924e-04 7780.391 3.742117e-04
## 91 GTR+G(4) 60 -3826.352 7772.704 1.197383e-04 7782.413 1.361863e-04
## 90 GTR+I 60 -3826.372 7772.745 1.173496e-04 7782.453 1.334695e-04
## 16 HKY+G(4)+I 57 -3831.107 7776.215 2.070147e-05 7784.949 3.831312e-05
## 36 TPM1u+G(4)+I 58 -3830.649 7777.297 1.204718e-05 7786.350 1.901450e-05
## 66 TIM2+I 58 -3830.708 7777.417 1.134976e-05 7786.470 1.791374e-05
## 75 TIM3+G(4) 58 -3831.138 7778.275 7.387967e-06 7787.328 1.166070e-05
## 67 TIM2+G(4) 58 -3831.158 7778.316 7.238093e-06 7787.369 1.142415e-05
## 83 TVM+G(4) 59 -3830.532 7779.063 4.982555e-06 7788.441 6.686079e-06
## 74 TIM3+I 58 -3832.285 7780.571 2.344369e-06 7789.624 3.700204e-06
## 82 TVM+I 59 -3831.448 7780.897 1.992003e-06 7790.274 2.673064e-06
## 51 TPM3u+G(4) 57 -3834.434 7782.869 7.431360e-07 7791.603 1.375354e-06
## 23 TrN+G(4) 57 -3834.876 7783.753 4.776779e-07 7792.487 8.840594e-07
## 43 TPM2u+G(4) 57 -3835.239 7784.479 3.322764e-07 7793.213 6.149584e-07
## 59 TIM1+G(4) 58 -3834.458 7784.916 2.670098e-07 7793.969 4.214314e-07
## 22 TrN+I 57 -3835.551 7785.102 2.433380e-07 7793.836 4.503562e-07
## 42 TPM2u+I 57 -3835.564 7785.128 2.401904e-07 7793.862 4.445309e-07
## 58 TIM1+I 58 -3835.136 7786.272 1.355647e-07 7795.325 2.139667e-07
## 50 TPM3u+I 57 -3836.594 7787.187 8.576882e-08 7795.922 1.587361e-07
## 15 HKY+G(4) 56 -3838.137 7788.274 4.981261e-08 7796.696 1.077715e-07
## 35 TPM1u+G(4) 57 -3837.719 7789.439 2.782580e-08 7798.173 5.149843e-08
## 14 HKY+I 56 -3839.720 7791.440 1.022806e-08 7799.862 2.212880e-08
## 34 TPM1u+I 57 -3839.307 7792.613 5.689277e-09 7801.348 1.052939e-08
## 88 SYM+G(4)+I 58 -3847.215 7810.431 7.691932e-13 7819.484 1.214046e-12
## 64 TIM2e+G(4)+I 56 -3852.888 7817.775 1.955508e-14 7826.197 4.230816e-14
## 86 SYM+I 57 -3855.407 7824.813 5.793534e-16 7833.548 1.072235e-15
## 62 TIM2e+I 55 -3861.020 7832.041 1.561429e-17 7840.157 3.937150e-17
## 87 SYM+G(4) 57 -3859.748 7833.496 7.542169e-18 7842.230 1.395862e-17
## 63 TIM2e+G(4) 55 -3865.431 7840.861 1.897184e-19 7848.977 4.783757e-19
## 72 TIM3e+G(4)+I 56 -3864.922 7841.845 1.160361e-19 7850.267 2.510485e-19
## 20 TrNe+G(4)+I 55 -3869.676 7849.352 2.718452e-21 7857.468 6.854589e-21
## 56 TIM1e+G(4)+I 56 -3869.253 7850.507 1.526387e-21 7858.929 3.302396e-21
## 70 TIM3e+I 55 -3875.762 7861.524 6.185701e-24 7869.640 1.559727e-23
## 71 TIM3e+G(4) 55 -3876.958 7863.916 1.869915e-24 7872.032 4.714998e-24
## 18 TrNe+I 54 -3880.283 7868.566 1.828357e-25 7876.382 5.356709e-25
## 54 TIM1e+I 55 -3879.892 7869.783 9.949979e-26 7877.899 2.508892e-25
## 19 TrNe+G(4) 54 -3881.555 7871.110 5.124203e-26 7878.926 1.501286e-25
## 55 TIM1e+G(4) 55 -3881.074 7872.148 3.049738e-26 7880.264 7.689927e-26
## 80 TVMe+G(4)+I 57 -3886.409 7886.818 1.990083e-29 7895.552 3.683133e-29
## 79 TVMe+G(4) 56 -3889.857 7891.714 1.720772e-30 7900.136 3.722955e-30
## 40 TPM2+G(4)+I 55 -3891.884 7893.767 6.163194e-31 7901.883 1.554052e-30
## 39 TPM2+G(4) 54 -3895.221 7898.443 5.949627e-32 7906.259 1.743118e-31
## 78 TVMe+I 56 -3898.607 7909.215 2.725193e-34 7917.637 5.896060e-34
## 48 TPM3+G(4)+I 55 -3899.630 7909.261 2.662870e-34 7917.377 6.714439e-34
## 47 TPM3+G(4) 54 -3902.727 7913.454 3.272598e-35 7921.270 9.588037e-35
## 38 TPM2+I 54 -3903.139 7914.278 2.167729e-35 7922.093 6.350998e-35
## 12 K80+G(4)+I 54 -3904.257 7916.514 7.084052e-36 7924.330 2.075481e-35
## 28 TPM1+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 32 K81+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 11 K80+G(4) 53 -3907.147 7920.293 1.070896e-36 7927.815 3.634535e-36
## 27 TPM1+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 31 K81+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 46 TPM3+I 54 -3910.077 7928.153 2.103725e-38 7935.969 6.163481e-38
## 10 K80+I 53 -3913.845 7933.691 1.319691e-39 7941.212 4.478927e-39
## 26 TPM1+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 30 K81+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 89 GTR 59 -4136.615 8391.231 5.847519e-139 8400.608 7.846774e-139
## 65 TIM2 57 -4139.239 8392.478 3.133793e-139 8401.213 5.799848e-139
## 85 SYM 56 -4146.395 8404.790 6.644955e-142 8413.213 1.437661e-141
## 61 TIM2e 54 -4149.681 8407.361 1.837467e-142 8415.177 5.383397e-142
## 81 TVM 58 -4155.419 8426.837 1.084222e-146 8435.890 1.711267e-146
## 41 TPM2u 56 -4158.175 8428.351 5.086543e-147 8436.773 1.100493e-146
## 73 TIM3 57 -4163.254 8440.508 1.165653e-149 8449.242 2.157326e-149
## 21 TrN 56 -4164.857 8441.714 6.377326e-150 8450.136 1.379759e-149
## 57 TIM1 57 -4164.146 8442.291 4.778564e-150 8451.026 8.843897e-150
## 49 TPM3u 56 -4182.147 8476.295 1.974906e-157 8484.717 4.272785e-157
## 69 TIM3e 54 -4184.626 8477.253 1.223344e-157 8485.068 3.584146e-157
## 13 HKY 55 -4183.735 8477.470 1.097208e-157 8485.586 2.766613e-157
## 33 TPM1u 56 -4183.048 8478.095 8.027521e-158 8486.517 1.736785e-157
## 17 TrNe 53 -4186.790 8479.579 3.822214e-158 8487.101 1.297229e-157
## 53 TIM1e 54 -4185.808 8479.616 3.751717e-158 8487.432 1.099175e-157
## 77 TVMe 55 -4192.004 8494.008 2.812296e-161 8502.124 7.091215e-161
## 37 TPM2 53 -4195.470 8496.940 6.491684e-162 8504.462 2.203226e-161
## 8 F81+G(4)+I 56 -4224.101 8560.203 1.188832e-175 8568.625 2.572083e-175
## 45 TPM3 53 -4230.129 8566.257 5.760596e-177 8573.779 1.955100e-176
## 6 F81+I 55 -4228.498 8566.996 3.980571e-177 8575.112 1.003703e-176
## 9 K80 52 -4232.278 8568.555 1.825468e-177 8575.789 7.155385e-177
## 25 TPM1 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 29 K81 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 7 F81+G(4) 55 -4230.284 8570.567 6.675493e-178 8578.683 1.683228e-177
## 4 JC+G(4)+I 53 -4284.782 8675.565 1.058262e-200 8683.086 3.591657e-200
## 2 JC+I 52 -4287.999 8679.998 1.153410e-201 8687.231 4.521083e-201
## 3 JC+G(4) 52 -4291.647 8687.293 3.004938e-203 8694.527 1.177862e-202
## 5 F81 54 -4506.634 9121.268 1.742945e-297 9129.084 5.106470e-297
## 1 JC 51 -4553.439 9208.877 1.649059e-316 9215.829 7.443029e-316
## BIC
## 92 8041.754
## 68 8037.657
## 76 8039.008
## 84 8048.552
## 24 8039.719
## 60 8045.555
## 52 8043.872
## 44 8044.123
## 91 8054.896
## 90 8054.936
## 16 8044.296
## 36 8050.082
## 66 8050.202
## 75 8051.060
## 67 8051.101
## 83 8056.551
## 74 8053.356
## 82 8058.385
## 51 8050.950
## 23 8051.834
## 43 8052.560
## 59 8057.701
## 22 8053.183
## 42 8053.209
## 58 8059.057
## 50 8055.269
## 15 8051.653
## 35 8057.520
## 14 8054.819
## 34 8060.695
## 88 8083.216
## 64 8081.154
## 86 8092.895
## 62 8090.716
## 87 8101.578
## 63 8099.537
## 72 8105.223
## 20 8108.028
## 56 8113.885
## 70 8120.199
## 71 8122.592
## 18 8122.539
## 54 8128.459
## 19 8125.083
## 55 8130.824
## 80 8154.899
## 79 8155.092
## 40 8152.442
## 39 8152.415
## 78 8172.593
## 48 8167.936
## 47 8167.426
## 38 8168.250
## 12 8170.487
## 28 8176.214
## 32 8176.214
## 11 8169.562
## 27 8175.380
## 31 8175.380
## 46 8182.125
## 10 8182.960
## 26 8188.986
## 30 8188.986
## 89 8668.719
## 65 8660.560
## 85 8668.169
## 61 8661.334
## 81 8699.622
## 41 8691.729
## 73 8708.589
## 21 8705.093
## 57 8710.373
## 49 8739.673
## 69 8731.225
## 13 8736.146
## 33 8741.474
## 17 8728.848
## 53 8733.589
## 77 8752.684
## 37 8746.209
## 8 8823.581
## 45 8815.526
## 6 8825.672
## 9 8813.121
## 25 8817.943
## 29 8817.943
## 7 8829.243
## 4 8924.834
## 2 8924.564
## 3 8931.859
## 5 9375.241
## 1 9448.740
mySequences_gr_ext_4_modelTest[order(mySequences_gr_ext_4_modelTest$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 68 TIM2+G(4)+I 59 -3821.085 7760.169 6.312408e-02 7769.547 8.470607e-02
## 76 TIM3+G(4)+I 59 -3821.760 7761.520 3.212413e-02 7770.898 4.310730e-02
## 24 TrN+G(4)+I 58 -3825.467 7766.934 2.144103e-03 7775.987 3.384116e-03
## 92 GTR+G(4)+I 61 -3816.430 7754.860 8.977207e-01 7764.905 8.627364e-01
## 52 TPM3u+G(4)+I 58 -3827.543 7771.087 2.688408e-04 7780.140 4.243213e-04
## 44 TPM2u+G(4)+I 58 -3827.669 7771.338 2.370924e-04 7780.391 3.742117e-04
## 16 HKY+G(4)+I 57 -3831.107 7776.215 2.070147e-05 7784.949 3.831312e-05
## 60 TIM1+G(4)+I 59 -3825.034 7768.067 1.216734e-03 7777.445 1.632733e-03
## 84 TVM+G(4)+I 60 -3823.180 7766.360 2.856606e-03 7776.068 3.249007e-03
## 36 TPM1u+G(4)+I 58 -3830.649 7777.297 1.204718e-05 7786.350 1.901450e-05
## 66 TIM2+I 58 -3830.708 7777.417 1.134976e-05 7786.470 1.791374e-05
## 51 TPM3u+G(4) 57 -3834.434 7782.869 7.431360e-07 7791.603 1.375354e-06
## 75 TIM3+G(4) 58 -3831.138 7778.275 7.387967e-06 7787.328 1.166070e-05
## 67 TIM2+G(4) 58 -3831.158 7778.316 7.238093e-06 7787.369 1.142415e-05
## 15 HKY+G(4) 56 -3838.137 7788.274 4.981261e-08 7796.696 1.077715e-07
## 23 TrN+G(4) 57 -3834.876 7783.753 4.776779e-07 7792.487 8.840594e-07
## 43 TPM2u+G(4) 57 -3835.239 7784.479 3.322764e-07 7793.213 6.149584e-07
## 22 TrN+I 57 -3835.551 7785.102 2.433380e-07 7793.836 4.503562e-07
## 42 TPM2u+I 57 -3835.564 7785.128 2.401904e-07 7793.862 4.445309e-07
## 74 TIM3+I 58 -3832.285 7780.571 2.344369e-06 7789.624 3.700204e-06
## 14 HKY+I 56 -3839.720 7791.440 1.022806e-08 7799.862 2.212880e-08
## 91 GTR+G(4) 60 -3826.352 7772.704 1.197383e-04 7782.413 1.361863e-04
## 90 GTR+I 60 -3826.372 7772.745 1.173496e-04 7782.453 1.334695e-04
## 50 TPM3u+I 57 -3836.594 7787.187 8.576882e-08 7795.922 1.587361e-07
## 83 TVM+G(4) 59 -3830.532 7779.063 4.982555e-06 7788.441 6.686079e-06
## 35 TPM1u+G(4) 57 -3837.719 7789.439 2.782580e-08 7798.173 5.149843e-08
## 59 TIM1+G(4) 58 -3834.458 7784.916 2.670098e-07 7793.969 4.214314e-07
## 82 TVM+I 59 -3831.448 7780.897 1.992003e-06 7790.274 2.673064e-06
## 58 TIM1+I 58 -3835.136 7786.272 1.355647e-07 7795.325 2.139667e-07
## 34 TPM1u+I 57 -3839.307 7792.613 5.689277e-09 7801.348 1.052939e-08
## 64 TIM2e+G(4)+I 56 -3852.888 7817.775 1.955508e-14 7826.197 4.230816e-14
## 88 SYM+G(4)+I 58 -3847.215 7810.431 7.691932e-13 7819.484 1.214046e-12
## 62 TIM2e+I 55 -3861.020 7832.041 1.561429e-17 7840.157 3.937150e-17
## 86 SYM+I 57 -3855.407 7824.813 5.793534e-16 7833.548 1.072235e-15
## 63 TIM2e+G(4) 55 -3865.431 7840.861 1.897184e-19 7848.977 4.783757e-19
## 87 SYM+G(4) 57 -3859.748 7833.496 7.542169e-18 7842.230 1.395862e-17
## 72 TIM3e+G(4)+I 56 -3864.922 7841.845 1.160361e-19 7850.267 2.510485e-19
## 20 TrNe+G(4)+I 55 -3869.676 7849.352 2.718452e-21 7857.468 6.854589e-21
## 56 TIM1e+G(4)+I 56 -3869.253 7850.507 1.526387e-21 7858.929 3.302396e-21
## 70 TIM3e+I 55 -3875.762 7861.524 6.185701e-24 7869.640 1.559727e-23
## 18 TrNe+I 54 -3880.283 7868.566 1.828357e-25 7876.382 5.356709e-25
## 71 TIM3e+G(4) 55 -3876.958 7863.916 1.869915e-24 7872.032 4.714998e-24
## 19 TrNe+G(4) 54 -3881.555 7871.110 5.124203e-26 7878.926 1.501286e-25
## 54 TIM1e+I 55 -3879.892 7869.783 9.949979e-26 7877.899 2.508892e-25
## 55 TIM1e+G(4) 55 -3881.074 7872.148 3.049738e-26 7880.264 7.689927e-26
## 39 TPM2+G(4) 54 -3895.221 7898.443 5.949627e-32 7906.259 1.743118e-31
## 40 TPM2+G(4)+I 55 -3891.884 7893.767 6.163194e-31 7901.883 1.554052e-30
## 80 TVMe+G(4)+I 57 -3886.409 7886.818 1.990083e-29 7895.552 3.683133e-29
## 79 TVMe+G(4) 56 -3889.857 7891.714 1.720772e-30 7900.136 3.722955e-30
## 47 TPM3+G(4) 54 -3902.727 7913.454 3.272598e-35 7921.270 9.588037e-35
## 48 TPM3+G(4)+I 55 -3899.630 7909.261 2.662870e-34 7917.377 6.714439e-34
## 38 TPM2+I 54 -3903.139 7914.278 2.167729e-35 7922.093 6.350998e-35
## 11 K80+G(4) 53 -3907.147 7920.293 1.070896e-36 7927.815 3.634535e-36
## 12 K80+G(4)+I 54 -3904.257 7916.514 7.084052e-36 7924.330 2.075481e-35
## 78 TVMe+I 56 -3898.607 7909.215 2.725193e-34 7917.637 5.896060e-34
## 27 TPM1+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 31 K81+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 28 TPM1+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 32 K81+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 46 TPM3+I 54 -3910.077 7928.153 2.103725e-38 7935.969 6.163481e-38
## 10 K80+I 53 -3913.845 7933.691 1.319691e-39 7941.212 4.478927e-39
## 26 TPM1+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 30 K81+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 65 TIM2 57 -4139.239 8392.478 3.133793e-139 8401.213 5.799848e-139
## 61 TIM2e 54 -4149.681 8407.361 1.837467e-142 8415.177 5.383397e-142
## 85 SYM 56 -4146.395 8404.790 6.644955e-142 8413.213 1.437661e-141
## 89 GTR 59 -4136.615 8391.231 5.847519e-139 8400.608 7.846774e-139
## 41 TPM2u 56 -4158.175 8428.351 5.086543e-147 8436.773 1.100493e-146
## 81 TVM 58 -4155.419 8426.837 1.084222e-146 8435.890 1.711267e-146
## 21 TrN 56 -4164.857 8441.714 6.377326e-150 8450.136 1.379759e-149
## 73 TIM3 57 -4163.254 8440.508 1.165653e-149 8449.242 2.157326e-149
## 57 TIM1 57 -4164.146 8442.291 4.778564e-150 8451.026 8.843897e-150
## 17 TrNe 53 -4186.790 8479.579 3.822214e-158 8487.101 1.297229e-157
## 69 TIM3e 54 -4184.626 8477.253 1.223344e-157 8485.068 3.584146e-157
## 53 TIM1e 54 -4185.808 8479.616 3.751717e-158 8487.432 1.099175e-157
## 13 HKY 55 -4183.735 8477.470 1.097208e-157 8485.586 2.766613e-157
## 49 TPM3u 56 -4182.147 8476.295 1.974906e-157 8484.717 4.272785e-157
## 33 TPM1u 56 -4183.048 8478.095 8.027521e-158 8486.517 1.736785e-157
## 37 TPM2 53 -4195.470 8496.940 6.491684e-162 8504.462 2.203226e-161
## 77 TVMe 55 -4192.004 8494.008 2.812296e-161 8502.124 7.091215e-161
## 9 K80 52 -4232.278 8568.555 1.825468e-177 8575.789 7.155385e-177
## 45 TPM3 53 -4230.129 8566.257 5.760596e-177 8573.779 1.955100e-176
## 25 TPM1 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 29 K81 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 8 F81+G(4)+I 56 -4224.101 8560.203 1.188832e-175 8568.625 2.572083e-175
## 6 F81+I 55 -4228.498 8566.996 3.980571e-177 8575.112 1.003703e-176
## 7 F81+G(4) 55 -4230.284 8570.567 6.675493e-178 8578.683 1.683228e-177
## 2 JC+I 52 -4287.999 8679.998 1.153410e-201 8687.231 4.521083e-201
## 4 JC+G(4)+I 53 -4284.782 8675.565 1.058262e-200 8683.086 3.591657e-200
## 3 JC+G(4) 52 -4291.647 8687.293 3.004938e-203 8694.527 1.177862e-202
## 5 F81 54 -4506.634 9121.268 1.742945e-297 9129.084 5.106470e-297
## 1 JC 51 -4553.439 9208.877 1.649059e-316 9215.829 7.443029e-316
## BIC
## 68 8037.657
## 76 8039.008
## 24 8039.719
## 92 8041.754
## 52 8043.872
## 44 8044.123
## 16 8044.296
## 60 8045.555
## 84 8048.552
## 36 8050.082
## 66 8050.202
## 51 8050.950
## 75 8051.060
## 67 8051.101
## 15 8051.653
## 23 8051.834
## 43 8052.560
## 22 8053.183
## 42 8053.209
## 74 8053.356
## 14 8054.819
## 91 8054.896
## 90 8054.936
## 50 8055.269
## 83 8056.551
## 35 8057.520
## 59 8057.701
## 82 8058.385
## 58 8059.057
## 34 8060.695
## 64 8081.154
## 88 8083.216
## 62 8090.716
## 86 8092.895
## 63 8099.537
## 87 8101.578
## 72 8105.223
## 20 8108.028
## 56 8113.885
## 70 8120.199
## 18 8122.539
## 71 8122.592
## 19 8125.083
## 54 8128.459
## 55 8130.824
## 39 8152.415
## 40 8152.442
## 80 8154.899
## 79 8155.092
## 47 8167.426
## 48 8167.936
## 38 8168.250
## 11 8169.562
## 12 8170.487
## 78 8172.593
## 27 8175.380
## 31 8175.380
## 28 8176.214
## 32 8176.214
## 46 8182.125
## 10 8182.960
## 26 8188.986
## 30 8188.986
## 65 8660.560
## 61 8661.334
## 85 8668.169
## 89 8668.719
## 41 8691.729
## 81 8699.622
## 21 8705.093
## 73 8708.589
## 57 8710.373
## 17 8728.848
## 69 8731.225
## 53 8733.589
## 13 8736.146
## 49 8739.673
## 33 8741.474
## 37 8746.209
## 77 8752.684
## 9 8813.121
## 45 8815.526
## 25 8817.943
## 29 8817.943
## 8 8823.581
## 6 8825.672
## 7 8829.243
## 2 8924.564
## 4 8924.834
## 3 8931.859
## 5 9375.241
## 1 9448.740
Meilleur modele: TIM2+G(4)+I
env$`TIM2+G(4)+I`
## pml(tree = `tree_TIM2+G(4)+I`, data = data, bf = c(0.271785050414015,
## 0.266095871120374, 0.168140595955613, 0.293978482509998), Q = c(3.37736920870854,
## 31.3229227038796, 3.37736920870854, 1, 56.2297502116579, 1),
## model = "TIM2", inv = 0.572671397044045, k = 4, shape = 2.48833057131467)
Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_4 = dist.logDet(mySequences_align_gr_ext_4_phangorn)
# Construction arbre NJ
treeNJ_gr_ext_4 <- NJ(mySequences_align_gr_ext_4)
# Visualisation
plot(treeNJ_gr_ext_4, main="Arbre NJ Groupe externe 4")
Integration des parametres
fit_gr_ext_4 = pml(treeNJ_gr_ext_4, data=mySequences_align_gr_ext_4_phangorn)
fitTIM2_gr_ext_4 <- update(fit_gr_ext_4, model="TIM2", k=4, inv=0.572669834174348, shape=2.4882559444008)
fitTIM2_gr_ext_4 <- optim.pml(fitTIM2_gr_ext_4, model="TIM2", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_gr_ext_4 = bootstrap.pml(fitTIM2_gr_ext_4, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTIM2_gr_ext_4$tree), bs_gr_ext_4, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Alignement
mySequences_align_aa_gr_ext_4 = AlignTranslation(Sequences_groupe_externe_4,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.05 secs
##
## Alignment converged - skipping remaining iteration.
Conversion
mySequences_align_aa_gr_ext_4_ape = as.AAbin(mySequences_align_aa_gr_ext_4)
mySequences_align_aa_gr_ext_4_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_4_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
Recherche du meilleur modele
mySequences_align_aa_gr_ext_4_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_4_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 51 -989.4844 2080.969 2263.919
## WAG+I 52 -978.0493 2060.099 2246.636
## WAG+G(4) 52 -979.044 2062.088 2248.625
## WAG+G(4)+I 53 -978.0852 2062.17 2252.295
## JTT 51 -985.0266 2072.053 2255.003
## JTT+I 52 -973.9716 2051.943 2238.48
## JTT+G(4) 52 -974.8447 2053.689 2240.226
## JTT+G(4)+I 53 -974.0697 2054.139 2244.263
## LG 51 -986.8872 2075.774 2258.724
## LG+I 52 -976.374 2056.748 2243.285
## LG+G(4) 52 -977.0353 2058.071 2244.607
## LG+G(4)+I 53 -976.3983 2058.797 2248.921
## Dayhoff 51 -1000.945 2103.889 2286.839
## Dayhoff+I 52 -989.3875 2082.775 2269.312
## Dayhoff+G(4) 52 -990.3689 2084.738 2271.275
## Dayhoff+G(4)+I 53 -989.579 2085.158 2275.282
## cpREV 51 -975.0217 2052.043 2234.993
## cpREV+I 52 -963.9911 2031.982 2218.519
## cpREV+G(4) 52 -964.818 2033.636 2220.173
## cpREV+G(4)+I 53 -964.1154 2034.231 2224.355
## mtmam 51 -945.8698 1993.74 2176.689
## mtmam+I 52 -936.5416 1977.083 2163.62
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## mtmam+G(4) 52 -936.6824 1977.365 2163.902
## mtmam+G(4)+I 53 -936.5512 1979.102 2169.227
## mtArt 51 -942.8977 1987.795 2170.745
## mtArt+I 52 -934.8133 1973.627 2160.164
## mtArt+G(4) 52 -934.9639 1973.928 2160.465
## mtArt+G(4)+I 53 -934.8252 1975.65 2165.775
## MtZoa 51 -937.3073 1976.615 2159.564
## MtZoa+I 52 -929.3564 1962.713 2149.25
## MtZoa+G(4) 52 -929.4937 1962.987 2149.524
## MtZoa+G(4)+I 53 -929.3668 1964.734 2154.858
## mtREV24 51 -949.6037 2001.207 2184.157
## mtREV24+I 52 -939.9664 1983.933 2170.47
## mtREV24+G(4) 52 -940.273 1984.546 2171.083
## mtREV24+G(4)+I 53 -939.9751 1985.95 2176.074
## VT 51 -978.9772 2059.954 2242.904
## VT+I 52 -969.715 2043.43 2229.967
## VT+G(4) 52 -970.0259 2044.052 2230.589
## VT+G(4)+I 53 -969.7784 2045.557 2235.681
## RtREV 51 -991.7055 2085.411 2268.361
## RtREV+I 52 -980.9445 2065.889 2252.426
## RtREV+G(4) 52 -981.5218 2067.044 2253.581
## RtREV+G(4)+I 53 -980.9558 2067.912 2258.036
## HIVw 51 -1024.179 2150.359 2333.308
## HIVw+I 52 -1008.35 2120.701 2307.238
## HIVw+G(4) 52 -1010.246 2124.493 2311.03
## HIVw+G(4)+I 53 -1008.504 2123.008 2313.133
## HIVb 51 -1001.539 2105.079 2288.028
## HIVb+I 52 -987.7643 2079.529 2266.065
## HIVb+G(4) 52 -989.0728 2082.146 2268.683
## HIVb+G(4)+I 53 -987.817 2081.634 2271.758
## FLU 51 -996.7898 2095.58 2278.529
## FLU+I 52 -985.172 2074.344 2260.881
## FLU+G(4) 52 -985.963 2075.926 2262.463
## FLU+G(4)+I 53 -985.282 2076.564 2266.688
## Blosum62 51 -984.9206 2071.841 2254.791
## Blosum62+I 52 -975.0209 2054.042 2240.579
## Blosum62+G(4) 52 -975.5213 2055.043 2241.58
## Blosum62+G(4)+I 53 -975.0382 2056.076 2246.201
## Dayhoff_DCMut 51 -1001.001 2104.001 2286.951
## Dayhoff_DCMut+I 52 -989.4565 2082.913 2269.45
## Dayhoff_DCMut+G(4) 52 -990.4347 2084.869 2271.406
## Dayhoff_DCMut+G(4)+I 53 -989.6481 2085.296 2275.42
## JTT_DCMut 51 -985.6565 2073.313 2256.263
## JTT_DCMut+I 52 -974.5499 2053.1 2239.637
## JTT_DCMut+G(4) 52 -975.4365 2054.873 2241.41
## JTT_DCMut+G(4)+I 53 -974.6698 2055.34 2245.464
Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_4_modeltest, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
mySequences_align_aa_gr_ext_4_modeltest[order(mySequences_align_aa_gr_ext_4_modeltest$AIC), ]
## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -929.3564 1962.713 4.448504e-01 1988.470
## 31 MtZoa+G(4) 52 -929.4937 1962.987 3.877679e-01 1988.744
## 32 MtZoa+G(4)+I 53 -929.3668 1964.734 1.619574e-01 1991.607
## 26 mtArt+I 52 -934.8133 1973.627 1.898024e-03 1999.384
## 27 mtArt+G(4) 52 -934.9639 1973.928 1.632722e-03 1999.685
## 28 mtArt+G(4)+I 53 -934.8252 1975.650 6.899977e-04 2002.524
## 29 MtZoa 51 -937.3073 1976.615 4.260545e-04 2001.284
## 22 mtmam+I 52 -936.5416 1977.083 3.370915e-04 2002.840
## 23 mtmam+G(4) 52 -936.6824 1977.365 2.928163e-04 2003.122
## 24 mtmam+G(4)+I 53 -936.5512 1979.102 1.228157e-04 2005.976
## 34 mtREV24+I 52 -939.9664 1983.933 1.097381e-05 2009.690
## 35 mtREV24+G(4) 52 -940.2730 1984.546 8.076048e-06 2010.303
## 36 mtREV24+G(4)+I 53 -939.9751 1985.950 4.002159e-06 2012.823
## 25 mtArt 51 -942.8977 1987.795 1.590768e-06 2012.465
## 21 mtmam 51 -945.8698 1993.740 8.144187e-08 2018.409
## 33 mtREV24 51 -949.6037 2001.207 1.946282e-09 2025.877
## 18 cpREV+I 52 -963.9911 2031.982 4.041605e-16 2057.739
## 19 cpREV+G(4) 52 -964.8180 2033.636 1.767838e-16 2059.393
## 20 cpREV+G(4)+I 53 -964.1154 2034.231 1.313106e-16 2061.104
## 38 VT+I 52 -969.7150 2043.430 1.320329e-18 2069.187
## 39 VT+G(4) 52 -970.0259 2044.052 9.675497e-19 2069.809
## 40 VT+G(4)+I 53 -969.7784 2045.557 4.559211e-19 2072.430
## 6 JTT+I 52 -973.9716 2051.943 1.870978e-20 2077.700
## 17 cpREV 51 -975.0217 2052.043 1.779666e-20 2076.713
## 66 JTT_DCMut+I 52 -974.5499 2053.100 1.049348e-20 2078.857
## 7 JTT+G(4) 52 -974.8447 2053.689 7.814648e-21 2079.446
## 58 Blosum62+I 52 -975.0209 2054.042 6.552254e-21 2079.799
## 8 JTT+G(4)+I 53 -974.0697 2054.139 6.240306e-21 2081.013
## 67 JTT_DCMut+G(4) 52 -975.4365 2054.873 4.323898e-21 2080.630
## 59 Blosum62+G(4) 52 -975.5213 2055.043 3.972329e-21 2080.800
## 68 JTT_DCMut+G(4)+I 53 -974.6698 2055.340 3.424422e-21 2082.213
## 60 Blosum62+G(4)+I 53 -975.0382 2056.076 2.369018e-21 2082.950
## 10 LG+I 52 -976.3740 2056.748 1.693243e-21 2082.505
## 11 LG+G(4) 52 -977.0353 2058.071 8.740773e-22 2083.828
## 12 LG+G(4)+I 53 -976.3983 2058.797 6.079550e-22 2085.670
## 37 VT 51 -978.9772 2059.954 3.407855e-22 2084.624
## 2 WAG+I 52 -978.0493 2060.099 3.170706e-22 2085.856
## 3 WAG+G(4) 52 -979.0440 2062.088 1.172617e-22 2087.845
## 4 WAG+G(4)+I 53 -978.0852 2062.170 1.125342e-22 2089.044
## 42 RtREV+I 52 -980.9445 2065.889 1.753017e-23 2091.646
## 43 RtREV+G(4) 52 -981.5218 2067.044 9.841342e-24 2092.801
## 44 RtREV+G(4)+I 53 -980.9558 2067.912 6.376483e-24 2094.785
## 57 Blosum62 51 -984.9206 2071.841 8.938842e-25 2096.511
## 5 JTT 51 -985.0266 2072.053 8.040085e-25 2096.723
## 65 JTT_DCMut 51 -985.6565 2073.313 4.282641e-25 2097.983
## 54 FLU+I 52 -985.1720 2074.344 2.557514e-25 2100.101
## 9 LG 51 -986.8872 2075.774 1.250836e-25 2100.444
## 55 FLU+G(4) 52 -985.9630 2075.926 1.159587e-25 2101.683
## 56 FLU+G(4)+I 53 -985.2820 2076.564 8.428459e-26 2103.437
## 50 HIVb+I 52 -987.7643 2079.529 1.914256e-26 2105.286
## 1 WAG 51 -989.4844 2080.969 9.316362e-27 2105.639
## 52 HIVb+G(4)+I 53 -987.8170 2081.634 6.680825e-27 2108.507
## 51 HIVb+G(4) 52 -989.0728 2082.146 5.172561e-27 2107.903
## 14 Dayhoff+I 52 -989.3875 2082.775 3.776241e-27 2108.532
## 62 Dayhoff_DCMut+I 52 -989.4565 2082.913 3.524502e-27 2108.670
## 15 Dayhoff+G(4) 52 -990.3689 2084.738 1.415238e-27 2110.495
## 63 Dayhoff_DCMut+G(4) 52 -990.4347 2084.869 1.325145e-27 2110.626
## 16 Dayhoff+G(4)+I 53 -989.5790 2085.158 1.147093e-27 2112.031
## 64 Dayhoff_DCMut+G(4)+I 53 -989.6481 2085.296 1.070455e-27 2112.169
## 41 RtREV 51 -991.7055 2085.411 1.010702e-27 2110.081
## 53 FLU 51 -996.7898 2095.580 6.259500e-30 2120.249
## 13 Dayhoff 51 -1000.9445 2103.889 9.821701e-32 2128.559
## 61 Dayhoff_DCMut 51 -1001.0005 2104.001 9.286583e-32 2128.671
## 49 HIVb 51 -1001.5393 2105.079 5.418406e-32 2129.748
## 46 HIVw+I 52 -1008.3504 2120.701 2.195655e-35 2146.458
## 48 HIVw+G(4)+I 53 -1008.5042 2123.008 6.925546e-36 2149.882
## 47 HIVw+G(4) 52 -1010.2463 2124.493 3.297493e-36 2150.250
## 45 HIVw 51 -1024.1793 2150.359 7.970257e-42 2175.028
## AICcw BIC
## 30 4.779801e-01 2149.250
## 31 4.166464e-01 2149.524
## 32 9.958875e-02 2154.858
## 26 2.039377e-03 2160.164
## 27 1.754317e-03 2160.465
## 28 4.242845e-04 2165.775
## 29 7.884106e-04 2159.564
## 22 3.621959e-04 2163.620
## 23 3.146234e-04 2163.902
## 24 7.552026e-05 2169.227
## 34 1.179107e-05 2170.470
## 35 8.677501e-06 2171.083
## 36 2.460956e-06 2176.074
## 25 2.943704e-06 2170.745
## 21 1.507076e-07 2176.689
## 33 3.601581e-09 2184.157
## 18 4.342598e-16 2218.519
## 19 1.899495e-16 2220.173
## 20 8.074384e-17 2224.355
## 38 1.418659e-18 2229.967
## 39 1.039607e-18 2230.589
## 40 2.803491e-19 2235.681
## 6 2.010316e-20 2238.480
## 17 3.293259e-20 2234.993
## 66 1.127497e-20 2239.637
## 7 8.396633e-21 2240.226
## 58 7.040224e-21 2240.579
## 8 3.837208e-21 2244.263
## 67 4.645915e-21 2241.410
## 59 4.268163e-21 2241.580
## 68 2.105701e-21 2245.464
## 60 1.456726e-21 2246.201
## 10 1.819345e-21 2243.285
## 11 9.391731e-22 2244.607
## 12 3.738358e-22 2248.921
## 37 6.306210e-22 2242.904
## 2 3.406840e-22 2246.636
## 3 1.259946e-22 2248.625
## 4 6.919809e-23 2252.295
## 42 1.883571e-23 2252.426
## 43 1.057426e-23 2253.581
## 44 3.920945e-24 2258.036
## 57 1.654126e-24 2254.791
## 5 1.487812e-24 2255.003
## 65 7.924995e-25 2256.263
## 54 2.747981e-25 2260.881
## 9 2.314662e-25 2258.724
## 55 1.245946e-25 2262.463
## 56 5.182719e-26 2266.688
## 50 2.056818e-26 2266.065
## 1 1.723986e-26 2263.919
## 52 4.108087e-27 2271.758
## 51 5.557781e-27 2268.683
## 14 4.057471e-27 2269.312
## 62 3.786984e-27 2269.450
## 15 1.520636e-27 2271.275
## 63 1.423833e-27 2271.406
## 16 7.053559e-28 2275.282
## 64 6.582307e-28 2275.420
## 41 1.870297e-27 2268.361
## 53 1.158316e-29 2278.529
## 13 1.817498e-31 2286.839
## 61 1.718475e-31 2286.951
## 49 1.002672e-31 2288.028
## 46 2.359173e-35 2307.238
## 48 4.258567e-36 2313.133
## 47 3.543069e-36 2311.030
## 45 1.474890e-41 2333.308
mySequences_align_aa_gr_ext_4_modeltest[order(mySequences_align_aa_gr_ext_4_modeltest$BIC), ]
## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -929.3564 1962.713 4.448504e-01 1988.470
## 31 MtZoa+G(4) 52 -929.4937 1962.987 3.877679e-01 1988.744
## 32 MtZoa+G(4)+I 53 -929.3668 1964.734 1.619574e-01 1991.607
## 29 MtZoa 51 -937.3073 1976.615 4.260545e-04 2001.284
## 26 mtArt+I 52 -934.8133 1973.627 1.898024e-03 1999.384
## 27 mtArt+G(4) 52 -934.9639 1973.928 1.632722e-03 1999.685
## 22 mtmam+I 52 -936.5416 1977.083 3.370915e-04 2002.840
## 23 mtmam+G(4) 52 -936.6824 1977.365 2.928163e-04 2003.122
## 28 mtArt+G(4)+I 53 -934.8252 1975.650 6.899977e-04 2002.524
## 24 mtmam+G(4)+I 53 -936.5512 1979.102 1.228157e-04 2005.976
## 34 mtREV24+I 52 -939.9664 1983.933 1.097381e-05 2009.690
## 25 mtArt 51 -942.8977 1987.795 1.590768e-06 2012.465
## 35 mtREV24+G(4) 52 -940.2730 1984.546 8.076048e-06 2010.303
## 36 mtREV24+G(4)+I 53 -939.9751 1985.950 4.002159e-06 2012.823
## 21 mtmam 51 -945.8698 1993.740 8.144187e-08 2018.409
## 33 mtREV24 51 -949.6037 2001.207 1.946282e-09 2025.877
## 18 cpREV+I 52 -963.9911 2031.982 4.041605e-16 2057.739
## 19 cpREV+G(4) 52 -964.8180 2033.636 1.767838e-16 2059.393
## 20 cpREV+G(4)+I 53 -964.1154 2034.231 1.313106e-16 2061.104
## 38 VT+I 52 -969.7150 2043.430 1.320329e-18 2069.187
## 39 VT+G(4) 52 -970.0259 2044.052 9.675497e-19 2069.809
## 17 cpREV 51 -975.0217 2052.043 1.779666e-20 2076.713
## 40 VT+G(4)+I 53 -969.7784 2045.557 4.559211e-19 2072.430
## 6 JTT+I 52 -973.9716 2051.943 1.870978e-20 2077.700
## 66 JTT_DCMut+I 52 -974.5499 2053.100 1.049348e-20 2078.857
## 7 JTT+G(4) 52 -974.8447 2053.689 7.814648e-21 2079.446
## 58 Blosum62+I 52 -975.0209 2054.042 6.552254e-21 2079.799
## 67 JTT_DCMut+G(4) 52 -975.4365 2054.873 4.323898e-21 2080.630
## 59 Blosum62+G(4) 52 -975.5213 2055.043 3.972329e-21 2080.800
## 37 VT 51 -978.9772 2059.954 3.407855e-22 2084.624
## 10 LG+I 52 -976.3740 2056.748 1.693243e-21 2082.505
## 8 JTT+G(4)+I 53 -974.0697 2054.139 6.240306e-21 2081.013
## 11 LG+G(4) 52 -977.0353 2058.071 8.740773e-22 2083.828
## 68 JTT_DCMut+G(4)+I 53 -974.6698 2055.340 3.424422e-21 2082.213
## 60 Blosum62+G(4)+I 53 -975.0382 2056.076 2.369018e-21 2082.950
## 2 WAG+I 52 -978.0493 2060.099 3.170706e-22 2085.856
## 3 WAG+G(4) 52 -979.0440 2062.088 1.172617e-22 2087.845
## 12 LG+G(4)+I 53 -976.3983 2058.797 6.079550e-22 2085.670
## 4 WAG+G(4)+I 53 -978.0852 2062.170 1.125342e-22 2089.044
## 42 RtREV+I 52 -980.9445 2065.889 1.753017e-23 2091.646
## 43 RtREV+G(4) 52 -981.5218 2067.044 9.841342e-24 2092.801
## 57 Blosum62 51 -984.9206 2071.841 8.938842e-25 2096.511
## 5 JTT 51 -985.0266 2072.053 8.040085e-25 2096.723
## 65 JTT_DCMut 51 -985.6565 2073.313 4.282641e-25 2097.983
## 44 RtREV+G(4)+I 53 -980.9558 2067.912 6.376483e-24 2094.785
## 9 LG 51 -986.8872 2075.774 1.250836e-25 2100.444
## 54 FLU+I 52 -985.1720 2074.344 2.557514e-25 2100.101
## 55 FLU+G(4) 52 -985.9630 2075.926 1.159587e-25 2101.683
## 1 WAG 51 -989.4844 2080.969 9.316362e-27 2105.639
## 50 HIVb+I 52 -987.7643 2079.529 1.914256e-26 2105.286
## 56 FLU+G(4)+I 53 -985.2820 2076.564 8.428459e-26 2103.437
## 41 RtREV 51 -991.7055 2085.411 1.010702e-27 2110.081
## 51 HIVb+G(4) 52 -989.0728 2082.146 5.172561e-27 2107.903
## 14 Dayhoff+I 52 -989.3875 2082.775 3.776241e-27 2108.532
## 62 Dayhoff_DCMut+I 52 -989.4565 2082.913 3.524502e-27 2108.670
## 15 Dayhoff+G(4) 52 -990.3689 2084.738 1.415238e-27 2110.495
## 63 Dayhoff_DCMut+G(4) 52 -990.4347 2084.869 1.325145e-27 2110.626
## 52 HIVb+G(4)+I 53 -987.8170 2081.634 6.680825e-27 2108.507
## 16 Dayhoff+G(4)+I 53 -989.5790 2085.158 1.147093e-27 2112.031
## 64 Dayhoff_DCMut+G(4)+I 53 -989.6481 2085.296 1.070455e-27 2112.169
## 53 FLU 51 -996.7898 2095.580 6.259500e-30 2120.249
## 13 Dayhoff 51 -1000.9445 2103.889 9.821701e-32 2128.559
## 61 Dayhoff_DCMut 51 -1001.0005 2104.001 9.286583e-32 2128.671
## 49 HIVb 51 -1001.5393 2105.079 5.418406e-32 2129.748
## 46 HIVw+I 52 -1008.3504 2120.701 2.195655e-35 2146.458
## 47 HIVw+G(4) 52 -1010.2463 2124.493 3.297493e-36 2150.250
## 48 HIVw+G(4)+I 53 -1008.5042 2123.008 6.925546e-36 2149.882
## 45 HIVw 51 -1024.1793 2150.359 7.970257e-42 2175.028
## AICcw BIC
## 30 4.779801e-01 2149.250
## 31 4.166464e-01 2149.524
## 32 9.958875e-02 2154.858
## 29 7.884106e-04 2159.564
## 26 2.039377e-03 2160.164
## 27 1.754317e-03 2160.465
## 22 3.621959e-04 2163.620
## 23 3.146234e-04 2163.902
## 28 4.242845e-04 2165.775
## 24 7.552026e-05 2169.227
## 34 1.179107e-05 2170.470
## 25 2.943704e-06 2170.745
## 35 8.677501e-06 2171.083
## 36 2.460956e-06 2176.074
## 21 1.507076e-07 2176.689
## 33 3.601581e-09 2184.157
## 18 4.342598e-16 2218.519
## 19 1.899495e-16 2220.173
## 20 8.074384e-17 2224.355
## 38 1.418659e-18 2229.967
## 39 1.039607e-18 2230.589
## 17 3.293259e-20 2234.993
## 40 2.803491e-19 2235.681
## 6 2.010316e-20 2238.480
## 66 1.127497e-20 2239.637
## 7 8.396633e-21 2240.226
## 58 7.040224e-21 2240.579
## 67 4.645915e-21 2241.410
## 59 4.268163e-21 2241.580
## 37 6.306210e-22 2242.904
## 10 1.819345e-21 2243.285
## 8 3.837208e-21 2244.263
## 11 9.391731e-22 2244.607
## 68 2.105701e-21 2245.464
## 60 1.456726e-21 2246.201
## 2 3.406840e-22 2246.636
## 3 1.259946e-22 2248.625
## 12 3.738358e-22 2248.921
## 4 6.919809e-23 2252.295
## 42 1.883571e-23 2252.426
## 43 1.057426e-23 2253.581
## 57 1.654126e-24 2254.791
## 5 1.487812e-24 2255.003
## 65 7.924995e-25 2256.263
## 44 3.920945e-24 2258.036
## 9 2.314662e-25 2258.724
## 54 2.747981e-25 2260.881
## 55 1.245946e-25 2262.463
## 1 1.723986e-26 2263.919
## 50 2.056818e-26 2266.065
## 56 5.182719e-26 2266.688
## 41 1.870297e-27 2268.361
## 51 5.557781e-27 2268.683
## 14 4.057471e-27 2269.312
## 62 3.786984e-27 2269.450
## 15 1.520636e-27 2271.275
## 63 1.423833e-27 2271.406
## 52 4.108087e-27 2271.758
## 16 7.053559e-28 2275.282
## 64 6.582307e-28 2275.420
## 53 1.158316e-29 2278.529
## 13 1.817498e-31 2286.839
## 61 1.718475e-31 2286.951
## 49 1.002672e-31 2288.028
## 46 2.359173e-35 2307.238
## 47 3.543069e-36 2311.030
## 48 4.258567e-36 2313.133
## 45 1.474890e-41 2333.308
Meilleur modele : MtZoa+I
env$`MtZoa+I`
## pml(tree = `tree_MtZoa+I`, data = data, model = "MtZoa", inv = 0.750243950421922)
Construction arbres
# Matrice de ditance
dm_aa_gr_ext_4 <- dist.ml(mySequences_align_aa_gr_ext_4_phangorn, model = "MtZoa")
# Construction arbre NJ
treeNJ_aa_gr_ext_4 <- NJ(dm_aa_gr_ext_4)
Integration des parametres
fit_aa_gr_ext_4 = pml(treeNJ_aa_gr_ext_4, data=mySequences_align_aa_gr_ext_4_phangorn)
fitMtZoa_aa_gr_ext_4 <- update(fit_aa_gr_ext_4, model="MtZoa", inv=0.7535778946048)
fitMtZoa_aa_gr_ext_4 <- optim.pml(fitMtZoa_aa_gr_ext_4, model="MtZoa", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_aa_gr_ext_4 = bootstrap.pml(fitMtZoa_aa_gr_ext_4, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitMtZoa_aa_gr_ext_4$tree), bs_aa_gr_ext_4, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Fusionner avec les cetaces
Sequences_groupe_externe_5 <- c(myNewSequences, myExterneSequences)
Alignement
mySequences_align_gr_ext_5 = AlignSeqs(Sequences_groupe_externe_5, gapOpening = c(-18,-16), gapExtension = c(-2,-1))
## Determining distance matrix based on shared 11-mers:
## ================================================================================
##
## Time difference of 0.02 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.7 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.61 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
Recherche du meilleur modele
mySequences_align_gr_ext_5_ape = as.DNAbin(mySequences_align_gr_ext_5)
mySequences_align_gr_ext_5_phangorn = as.phyDat(mySequences_align_gr_ext_5_ape)
mySequences_gr_ext_5_modelTest = phangorn::modelTest(mySequences_align_gr_ext_5_phangorn)
## Model df logLik AIC BIC
## JC 63 -32775.4 65676.79 66162.25
## JC+I 64 -32237.33 64602.66 65095.83
## JC+G(4) 64 -32237.07 64602.14 65095.31
## JC+G(4)+I 65 -32223.44 64576.88 65077.75
## F81 66 -32078.43 64288.86 64797.44
## F81+I 67 -31508.49 63150.97 63667.25
## F81+G(4) 67 -31502.67 63139.33 63655.61
## F81+G(4)+I 68 -31491.05 63118.1 63642.09
## K80 64 -31738.74 63605.47 64098.64
## K80+I 65 -31131.18 62392.35 62893.22
## K80+G(4) 65 -31079.78 62289.57 62790.43
## K80+G(4)+I 66 -31074.41 62280.82 62789.39
## HKY 67 -31004.41 62142.81 62659.09
## HKY+I 68 -30302.17 60740.35 61264.33
## HKY+G(4) 68 -30240.26 60616.52 61140.5
## HKY+G(4)+I 69 -30233.94 60605.89 61137.58
## TrNe 65 -31696.4 63522.8 64023.66
## TrNe+I 66 -31089.78 62311.56 62820.14
## TrNe+G(4) 66 -31056.75 62245.5 62754.07
## TrNe+G(4)+I 67 -31042.66 62219.32 62735.6
## TrN 68 -30999.16 62134.31 62658.29
## TrN+I 69 -30301.63 60741.27 61272.96
## TrN+G(4) 69 -30240.22 60618.45 61150.14
## TrN+G(4)+I 70 -30233.7 60607.41 61146.8
## TPM1 65 -31738.74 63607.47 64108.34
## TPM1+I 66 -31131.17 62394.34 62902.91
## TPM1+G(4) 66 -31079.74 62291.47 62800.04
## TPM1+G(4)+I 67 -31074.38 62282.76 62799.04
## K81 65 -31738.74 63607.47 64108.34
## K81+I 66 -31131.17 62394.34 62902.91
## K81+G(4) 66 -31079.74 62291.47 62800.04
## K81+G(4)+I 67 -31074.38 62282.76 62799.04
## TPM1u 68 -31004.4 62144.8 62668.78
## TPM1u+I 69 -30302.04 60742.08 61273.77
## TPM1u+G(4) 69 -30240.09 60618.17 61149.86
## TPM1u+G(4)+I 70 -30233.72 60607.43 61146.83
## TPM2 65 -31674.86 63479.71 63980.58
## TPM2+I 66 -31098.51 62329.02 62837.6
## TPM2+G(4) 66 -31060.17 62252.33 62760.9
## TPM2+G(4)+I 67 -31051.86 62237.71 62753.99
## TPM2u 68 -30973.91 62083.82 62607.8
## TPM2u+I 69 -30295.92 60729.84 61261.53
## TPM2u+G(4) 69 -30238.74 60615.48 61147.17
## TPM2u+G(4)+I 70 -30231.98 60603.96 61143.36
## TPM3 65 -31737.58 63605.17 64106.03
## TPM3+I 66 -31126.63 62385.25 62893.82
## TPM3+G(4) 66 -31077.06 62286.12 62794.69
## TPM3+G(4)+I 67 -31071.43 62276.86 62793.14
## TPM3u 68 -31002.89 62141.77 62665.76
## TPM3u+I 69 -30298.72 60735.45 61267.14
## TPM3u+G(4) 69 -30238.04 60614.08 61145.77
## TPM3u+G(4)+I 70 -30231.37 60602.74 61142.14
## TIM1e 66 -31696.4 63524.8 64033.37
## TIM1e+I 67 -31089.78 62313.55 62829.83
## TIM1e+G(4) 67 -31056.73 62247.46 62763.74
## TIM1e+G(4)+I 68 -31042.65 62221.3 62745.28
## TIM1 69 -30999.15 62136.3 62667.99
## TIM1+I 70 -30301.51 60743.02 61282.41
## TIM1+G(4) 70 -30240.05 60620.1 61159.49
## TIM1+G(4)+I 71 -30233.48 60608.97 61156.07
## TIM2e 66 -31632.21 63396.43 63905
## TIM2e+I 67 -31051.59 62237.18 62753.45
## TIM2e+G(4) 67 -31032.95 62199.91 62716.18
## TIM2e+G(4)+I 68 -31015.47 62166.95 62690.93
## TIM2 69 -30968.65 62075.3 62606.99
## TIM2+I 70 -30294.96 60729.92 61269.32
## TIM2+G(4) 70 -30238.73 60617.46 61156.86
## TIM2+G(4)+I 71 -30231.62 60605.25 61152.35
## TIM3e 66 -31695.21 63522.42 64030.99
## TIM3e+I 67 -31085.09 62304.19 62820.47
## TIM3e+G(4) 67 -31054.27 62242.54 62758.82
## TIM3e+G(4)+I 68 -31039.84 62215.68 62739.66
## TIM3 69 -30997.62 62133.24 62664.93
## TIM3+I 70 -30298.17 60736.35 61275.74
## TIM3+G(4) 70 -30237.99 60615.99 61155.38
## TIM3+G(4)+I 71 -30231.15 60604.29 61151.39
## TVMe 67 -31673.13 63480.26 63996.54
## TVMe+I 68 -31093.79 62323.58 62847.57
## TVMe+G(4) 68 -31057.02 62250.04 62774.03
## TVMe+G(4)+I 69 -31048.64 62235.27 62766.96
## TVM 70 -30971.65 62083.3 62622.69
## TVM+I 71 -30291.76 60725.53 61272.63
## TVM+G(4) 71 -30236.27 60614.54 61161.64
## TVM+G(4)+I 72 -30229.22 60602.44 61157.25
## SYM 68 -31630.42 63396.84 63920.83
## SYM+I 69 -31046.8 62231.61 62763.3
## SYM+G(4) 69 -31030.03 62198.05 62729.74
## SYM+G(4)+I 70 -31012.39 62164.78 62704.18
## GTR 71 -30966.37 62074.74 62621.84
## GTR+I 72 -30290.79 60725.59 61280.4
## GTR+G(4) 72 -30236.26 60616.51 61171.32
## GTR+G(4)+I 73 -30228.88 60603.76 61166.27
Trouver le meilleur modele
env <- attr(mySequences_gr_ext_5_modelTest, "env")
ls(env=env)
## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"
mySequences_gr_ext_5_modelTest[order(mySequences_gr_ext_5_modelTest$AIC), ]
## Model df logLik AIC AICw AICc AICcw
## 84 TVM+G(4)+I 72 -30229.22 60602.44 2.576621e-01 60603.09 2.555028e-01
## 52 TPM3u+G(4)+I 70 -30231.37 60602.74 2.215058e-01 60603.35 2.235370e-01
## 92 GTR+G(4)+I 73 -30228.88 60603.76 1.333119e-01 60604.42 1.310159e-01
## 44 TPM2u+G(4)+I 70 -30231.98 60603.96 1.204924e-01 60604.57 1.215973e-01
## 76 TIM3+G(4)+I 71 -30231.15 60604.29 1.022371e-01 60604.92 1.022798e-01
## 68 TIM2+G(4)+I 71 -30231.62 60605.25 6.335246e-02 60605.87 6.337894e-02
## 16 HKY+G(4)+I 69 -30233.94 60605.89 4.597245e-02 60606.48 4.679408e-02
## 24 TrN+G(4)+I 70 -30233.70 60607.41 2.150824e-02 60608.02 2.170547e-02
## 36 TPM1u+G(4)+I 70 -30233.72 60607.43 2.122298e-02 60608.04 2.141759e-02
## 60 TIM1+G(4)+I 71 -30233.48 60608.97 9.867728e-03 60609.59 9.871852e-03
## 51 TPM3u+G(4) 69 -30238.04 60614.08 7.665745e-04 60614.67 7.802749e-04
## 83 TVM+G(4) 71 -30236.27 60614.54 6.094845e-04 60615.16 6.097392e-04
## 43 TPM2u+G(4) 69 -30238.74 60615.48 3.793342e-04 60616.07 3.861137e-04
## 75 TIM3+G(4) 70 -30237.99 60615.99 2.946165e-04 60616.60 2.973180e-04
## 91 GTR+G(4) 72 -30236.26 60616.51 2.268411e-04 60617.16 2.249401e-04
## 15 HKY+G(4) 68 -30240.26 60616.52 2.262507e-04 60617.09 2.322516e-04
## 67 TIM2+G(4) 70 -30238.73 60617.46 1.408620e-04 60618.07 1.421537e-04
## 35 TPM1u+G(4) 69 -30240.09 60618.17 9.879058e-05 60618.77 1.005562e-04
## 23 TrN+G(4) 69 -30240.22 60618.45 8.625433e-05 60619.04 8.779589e-05
## 59 TIM1+G(4) 70 -30240.05 60620.10 3.778567e-05 60620.70 3.813215e-05
## 82 TVM+I 71 -30291.76 60725.53 4.827230e-28 60726.15 4.829248e-28
## 90 GTR+I 72 -30290.79 60725.59 4.676748e-28 60726.23 4.637556e-28
## 42 TPM2u+I 69 -30295.92 60729.84 5.576489e-29 60730.43 5.676154e-29
## 66 TIM2+I 70 -30294.96 60729.92 5.356339e-29 60730.53 5.405454e-29
## 50 TPM3u+I 69 -30298.72 60735.45 3.377990e-30 60736.04 3.438362e-30
## 74 TIM3+I 70 -30298.17 60736.35 2.156340e-30 60736.96 2.176113e-30
## 14 HKY+I 68 -30302.17 60740.35 2.918886e-31 60740.92 2.996305e-31
## 22 TrN+I 69 -30301.63 60741.27 1.842596e-31 60741.86 1.875528e-31
## 34 TPM1u+I 69 -30302.04 60742.08 1.225962e-31 60742.67 1.247873e-31
## 58 TIM1+I 70 -30301.51 60743.02 7.689664e-32 60743.62 7.760176e-32
## 89 GTR 71 -30966.37 62074.74 5.069114e-321 62075.37 5.074054e-321
## 65 TIM2 69 -30968.65 62075.30 3.833949e-321 62075.89 3.903119e-321
## 81 TVM 70 -30971.65 62083.30 6.916919e-323 62083.91 6.916919e-323
## 41 TPM2u 68 -30973.91 62083.82 5.434722e-323 62084.39 5.434722e-323
## 73 TIM3 69 -30997.62 62133.24 0.000000e+00 62133.83 0.000000e+00
## 21 TrN 68 -30999.16 62134.31 0.000000e+00 62134.88 0.000000e+00
## 57 TIM1 69 -30999.15 62136.30 0.000000e+00 62136.89 0.000000e+00
## 49 TPM3u 68 -31002.89 62141.77 0.000000e+00 62142.35 0.000000e+00
## 13 HKY 67 -31004.41 62142.81 0.000000e+00 62143.37 0.000000e+00
## 33 TPM1u 68 -31004.40 62144.80 0.000000e+00 62145.37 0.000000e+00
## 88 SYM+G(4)+I 70 -31012.39 62164.78 0.000000e+00 62165.39 0.000000e+00
## 64 TIM2e+G(4)+I 68 -31015.47 62166.95 0.000000e+00 62167.52 0.000000e+00
## 87 SYM+G(4) 69 -31030.03 62198.05 0.000000e+00 62198.64 0.000000e+00
## 63 TIM2e+G(4) 67 -31032.95 62199.91 0.000000e+00 62200.46 0.000000e+00
## 72 TIM3e+G(4)+I 68 -31039.84 62215.68 0.000000e+00 62216.25 0.000000e+00
## 20 TrNe+G(4)+I 67 -31042.66 62219.32 0.000000e+00 62219.88 0.000000e+00
## 56 TIM1e+G(4)+I 68 -31042.65 62221.30 0.000000e+00 62221.87 0.000000e+00
## 86 SYM+I 69 -31046.80 62231.61 0.000000e+00 62232.20 0.000000e+00
## 80 TVMe+G(4)+I 69 -31048.64 62235.27 0.000000e+00 62235.87 0.000000e+00
## 62 TIM2e+I 67 -31051.59 62237.18 0.000000e+00 62237.73 0.000000e+00
## 40 TPM2+G(4)+I 67 -31051.86 62237.71 0.000000e+00 62238.27 0.000000e+00
## 71 TIM3e+G(4) 67 -31054.27 62242.54 0.000000e+00 62243.10 0.000000e+00
## 19 TrNe+G(4) 66 -31056.75 62245.50 0.000000e+00 62246.04 0.000000e+00
## 55 TIM1e+G(4) 67 -31056.73 62247.46 0.000000e+00 62248.02 0.000000e+00
## 79 TVMe+G(4) 68 -31057.02 62250.04 0.000000e+00 62250.62 0.000000e+00
## 39 TPM2+G(4) 66 -31060.17 62252.33 0.000000e+00 62252.87 0.000000e+00
## 48 TPM3+G(4)+I 67 -31071.43 62276.86 0.000000e+00 62277.41 0.000000e+00
## 12 K80+G(4)+I 66 -31074.41 62280.82 0.000000e+00 62281.36 0.000000e+00
## 28 TPM1+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 32 K81+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 47 TPM3+G(4) 66 -31077.06 62286.12 0.000000e+00 62286.66 0.000000e+00
## 11 K80+G(4) 65 -31079.78 62289.57 0.000000e+00 62290.09 0.000000e+00
## 27 TPM1+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 31 K81+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 70 TIM3e+I 67 -31085.09 62304.19 0.000000e+00 62304.75 0.000000e+00
## 18 TrNe+I 66 -31089.78 62311.56 0.000000e+00 62312.10 0.000000e+00
## 54 TIM1e+I 67 -31089.78 62313.55 0.000000e+00 62314.11 0.000000e+00
## 78 TVMe+I 68 -31093.79 62323.58 0.000000e+00 62324.16 0.000000e+00
## 38 TPM2+I 66 -31098.51 62329.02 0.000000e+00 62329.57 0.000000e+00
## 46 TPM3+I 66 -31126.63 62385.25 0.000000e+00 62385.79 0.000000e+00
## 10 K80+I 65 -31131.18 62392.35 0.000000e+00 62392.88 0.000000e+00
## 26 TPM1+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 30 K81+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 8 F81+G(4)+I 68 -31491.05 63118.10 0.000000e+00 63118.68 0.000000e+00
## 7 F81+G(4) 67 -31502.67 63139.33 0.000000e+00 63139.89 0.000000e+00
## 6 F81+I 67 -31508.49 63150.97 0.000000e+00 63151.53 0.000000e+00
## 61 TIM2e 66 -31632.21 63396.43 0.000000e+00 63396.97 0.000000e+00
## 85 SYM 68 -31630.42 63396.84 0.000000e+00 63397.42 0.000000e+00
## 37 TPM2 65 -31674.86 63479.71 0.000000e+00 63480.24 0.000000e+00
## 77 TVMe 67 -31673.13 63480.26 0.000000e+00 63480.82 0.000000e+00
## 69 TIM3e 66 -31695.21 63522.42 0.000000e+00 63522.96 0.000000e+00
## 17 TrNe 65 -31696.40 63522.80 0.000000e+00 63523.32 0.000000e+00
## 53 TIM1e 66 -31696.40 63524.80 0.000000e+00 63525.34 0.000000e+00
## 45 TPM3 65 -31737.58 63605.17 0.000000e+00 63605.69 0.000000e+00
## 9 K80 64 -31738.74 63605.47 0.000000e+00 63605.98 0.000000e+00
## 25 TPM1 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 29 K81 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 5 F81 66 -32078.43 64288.86 0.000000e+00 64289.40 0.000000e+00
## 4 JC+G(4)+I 65 -32223.44 64576.88 0.000000e+00 64577.40 0.000000e+00
## 3 JC+G(4) 64 -32237.07 64602.14 0.000000e+00 64602.65 0.000000e+00
## 2 JC+I 64 -32237.33 64602.66 0.000000e+00 64603.17 0.000000e+00
## 1 JC 63 -32775.40 65676.79 0.000000e+00 65677.29 0.000000e+00
## BIC
## 84 61157.25
## 52 61142.14
## 92 61166.27
## 44 61143.36
## 76 61151.39
## 68 61152.35
## 16 61137.58
## 24 61146.80
## 36 61146.83
## 60 61156.07
## 51 61145.77
## 83 61161.64
## 43 61147.17
## 75 61155.38
## 91 61171.32
## 15 61140.50
## 67 61156.86
## 35 61149.86
## 23 61150.14
## 59 61159.49
## 82 61272.63
## 90 61280.40
## 42 61261.53
## 66 61269.32
## 50 61267.14
## 74 61275.74
## 14 61264.33
## 22 61272.96
## 34 61273.77
## 58 61282.41
## 89 62621.84
## 65 62606.99
## 81 62622.69
## 41 62607.80
## 73 62664.93
## 21 62658.29
## 57 62667.99
## 49 62665.76
## 13 62659.09
## 33 62668.78
## 88 62704.18
## 64 62690.93
## 87 62729.74
## 63 62716.18
## 72 62739.66
## 20 62735.60
## 56 62745.28
## 86 62763.30
## 80 62766.96
## 62 62753.45
## 40 62753.99
## 71 62758.82
## 19 62754.07
## 55 62763.74
## 79 62774.03
## 39 62760.90
## 48 62793.14
## 12 62789.39
## 28 62799.04
## 32 62799.04
## 47 62794.69
## 11 62790.43
## 27 62800.04
## 31 62800.04
## 70 62820.47
## 18 62820.14
## 54 62829.83
## 78 62847.57
## 38 62837.60
## 46 62893.82
## 10 62893.22
## 26 62902.91
## 30 62902.91
## 8 63642.09
## 7 63655.61
## 6 63667.25
## 61 63905.00
## 85 63920.83
## 37 63980.58
## 77 63996.54
## 69 64030.99
## 17 64023.66
## 53 64033.37
## 45 64106.03
## 9 64098.64
## 25 64108.34
## 29 64108.34
## 5 64797.44
## 4 65077.75
## 3 65095.31
## 2 65095.83
## 1 66162.25
mySequences_gr_ext_5_modelTest[order(mySequences_gr_ext_5_modelTest$BIC), ]
## Model df logLik AIC AICw AICc AICcw
## 16 HKY+G(4)+I 69 -30233.94 60605.89 4.597245e-02 60606.48 4.679408e-02
## 15 HKY+G(4) 68 -30240.26 60616.52 2.262507e-04 60617.09 2.322516e-04
## 52 TPM3u+G(4)+I 70 -30231.37 60602.74 2.215058e-01 60603.35 2.235370e-01
## 44 TPM2u+G(4)+I 70 -30231.98 60603.96 1.204924e-01 60604.57 1.215973e-01
## 51 TPM3u+G(4) 69 -30238.04 60614.08 7.665745e-04 60614.67 7.802749e-04
## 24 TrN+G(4)+I 70 -30233.70 60607.41 2.150824e-02 60608.02 2.170547e-02
## 36 TPM1u+G(4)+I 70 -30233.72 60607.43 2.122298e-02 60608.04 2.141759e-02
## 43 TPM2u+G(4) 69 -30238.74 60615.48 3.793342e-04 60616.07 3.861137e-04
## 35 TPM1u+G(4) 69 -30240.09 60618.17 9.879058e-05 60618.77 1.005562e-04
## 23 TrN+G(4) 69 -30240.22 60618.45 8.625433e-05 60619.04 8.779589e-05
## 76 TIM3+G(4)+I 71 -30231.15 60604.29 1.022371e-01 60604.92 1.022798e-01
## 68 TIM2+G(4)+I 71 -30231.62 60605.25 6.335246e-02 60605.87 6.337894e-02
## 75 TIM3+G(4) 70 -30237.99 60615.99 2.946165e-04 60616.60 2.973180e-04
## 60 TIM1+G(4)+I 71 -30233.48 60608.97 9.867728e-03 60609.59 9.871852e-03
## 67 TIM2+G(4) 70 -30238.73 60617.46 1.408620e-04 60618.07 1.421537e-04
## 84 TVM+G(4)+I 72 -30229.22 60602.44 2.576621e-01 60603.09 2.555028e-01
## 59 TIM1+G(4) 70 -30240.05 60620.10 3.778567e-05 60620.70 3.813215e-05
## 83 TVM+G(4) 71 -30236.27 60614.54 6.094845e-04 60615.16 6.097392e-04
## 92 GTR+G(4)+I 73 -30228.88 60603.76 1.333119e-01 60604.42 1.310159e-01
## 91 GTR+G(4) 72 -30236.26 60616.51 2.268411e-04 60617.16 2.249401e-04
## 42 TPM2u+I 69 -30295.92 60729.84 5.576489e-29 60730.43 5.676154e-29
## 14 HKY+I 68 -30302.17 60740.35 2.918886e-31 60740.92 2.996305e-31
## 50 TPM3u+I 69 -30298.72 60735.45 3.377990e-30 60736.04 3.438362e-30
## 66 TIM2+I 70 -30294.96 60729.92 5.356339e-29 60730.53 5.405454e-29
## 82 TVM+I 71 -30291.76 60725.53 4.827230e-28 60726.15 4.829248e-28
## 22 TrN+I 69 -30301.63 60741.27 1.842596e-31 60741.86 1.875528e-31
## 34 TPM1u+I 69 -30302.04 60742.08 1.225962e-31 60742.67 1.247873e-31
## 74 TIM3+I 70 -30298.17 60736.35 2.156340e-30 60736.96 2.176113e-30
## 90 GTR+I 72 -30290.79 60725.59 4.676748e-28 60726.23 4.637556e-28
## 58 TIM1+I 70 -30301.51 60743.02 7.689664e-32 60743.62 7.760176e-32
## 65 TIM2 69 -30968.65 62075.30 3.833949e-321 62075.89 3.903119e-321
## 41 TPM2u 68 -30973.91 62083.82 5.434722e-323 62084.39 5.434722e-323
## 89 GTR 71 -30966.37 62074.74 5.069114e-321 62075.37 5.074054e-321
## 81 TVM 70 -30971.65 62083.30 6.916919e-323 62083.91 6.916919e-323
## 21 TrN 68 -30999.16 62134.31 0.000000e+00 62134.88 0.000000e+00
## 13 HKY 67 -31004.41 62142.81 0.000000e+00 62143.37 0.000000e+00
## 73 TIM3 69 -30997.62 62133.24 0.000000e+00 62133.83 0.000000e+00
## 49 TPM3u 68 -31002.89 62141.77 0.000000e+00 62142.35 0.000000e+00
## 57 TIM1 69 -30999.15 62136.30 0.000000e+00 62136.89 0.000000e+00
## 33 TPM1u 68 -31004.40 62144.80 0.000000e+00 62145.37 0.000000e+00
## 64 TIM2e+G(4)+I 68 -31015.47 62166.95 0.000000e+00 62167.52 0.000000e+00
## 88 SYM+G(4)+I 70 -31012.39 62164.78 0.000000e+00 62165.39 0.000000e+00
## 63 TIM2e+G(4) 67 -31032.95 62199.91 0.000000e+00 62200.46 0.000000e+00
## 87 SYM+G(4) 69 -31030.03 62198.05 0.000000e+00 62198.64 0.000000e+00
## 20 TrNe+G(4)+I 67 -31042.66 62219.32 0.000000e+00 62219.88 0.000000e+00
## 72 TIM3e+G(4)+I 68 -31039.84 62215.68 0.000000e+00 62216.25 0.000000e+00
## 56 TIM1e+G(4)+I 68 -31042.65 62221.30 0.000000e+00 62221.87 0.000000e+00
## 62 TIM2e+I 67 -31051.59 62237.18 0.000000e+00 62237.73 0.000000e+00
## 40 TPM2+G(4)+I 67 -31051.86 62237.71 0.000000e+00 62238.27 0.000000e+00
## 19 TrNe+G(4) 66 -31056.75 62245.50 0.000000e+00 62246.04 0.000000e+00
## 71 TIM3e+G(4) 67 -31054.27 62242.54 0.000000e+00 62243.10 0.000000e+00
## 39 TPM2+G(4) 66 -31060.17 62252.33 0.000000e+00 62252.87 0.000000e+00
## 86 SYM+I 69 -31046.80 62231.61 0.000000e+00 62232.20 0.000000e+00
## 55 TIM1e+G(4) 67 -31056.73 62247.46 0.000000e+00 62248.02 0.000000e+00
## 80 TVMe+G(4)+I 69 -31048.64 62235.27 0.000000e+00 62235.87 0.000000e+00
## 79 TVMe+G(4) 68 -31057.02 62250.04 0.000000e+00 62250.62 0.000000e+00
## 12 K80+G(4)+I 66 -31074.41 62280.82 0.000000e+00 62281.36 0.000000e+00
## 11 K80+G(4) 65 -31079.78 62289.57 0.000000e+00 62290.09 0.000000e+00
## 48 TPM3+G(4)+I 67 -31071.43 62276.86 0.000000e+00 62277.41 0.000000e+00
## 47 TPM3+G(4) 66 -31077.06 62286.12 0.000000e+00 62286.66 0.000000e+00
## 28 TPM1+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 32 K81+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 27 TPM1+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 31 K81+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 18 TrNe+I 66 -31089.78 62311.56 0.000000e+00 62312.10 0.000000e+00
## 70 TIM3e+I 67 -31085.09 62304.19 0.000000e+00 62304.75 0.000000e+00
## 54 TIM1e+I 67 -31089.78 62313.55 0.000000e+00 62314.11 0.000000e+00
## 38 TPM2+I 66 -31098.51 62329.02 0.000000e+00 62329.57 0.000000e+00
## 78 TVMe+I 68 -31093.79 62323.58 0.000000e+00 62324.16 0.000000e+00
## 10 K80+I 65 -31131.18 62392.35 0.000000e+00 62392.88 0.000000e+00
## 46 TPM3+I 66 -31126.63 62385.25 0.000000e+00 62385.79 0.000000e+00
## 26 TPM1+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 30 K81+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 8 F81+G(4)+I 68 -31491.05 63118.10 0.000000e+00 63118.68 0.000000e+00
## 7 F81+G(4) 67 -31502.67 63139.33 0.000000e+00 63139.89 0.000000e+00
## 6 F81+I 67 -31508.49 63150.97 0.000000e+00 63151.53 0.000000e+00
## 61 TIM2e 66 -31632.21 63396.43 0.000000e+00 63396.97 0.000000e+00
## 85 SYM 68 -31630.42 63396.84 0.000000e+00 63397.42 0.000000e+00
## 37 TPM2 65 -31674.86 63479.71 0.000000e+00 63480.24 0.000000e+00
## 77 TVMe 67 -31673.13 63480.26 0.000000e+00 63480.82 0.000000e+00
## 17 TrNe 65 -31696.40 63522.80 0.000000e+00 63523.32 0.000000e+00
## 69 TIM3e 66 -31695.21 63522.42 0.000000e+00 63522.96 0.000000e+00
## 53 TIM1e 66 -31696.40 63524.80 0.000000e+00 63525.34 0.000000e+00
## 9 K80 64 -31738.74 63605.47 0.000000e+00 63605.98 0.000000e+00
## 45 TPM3 65 -31737.58 63605.17 0.000000e+00 63605.69 0.000000e+00
## 25 TPM1 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 29 K81 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 5 F81 66 -32078.43 64288.86 0.000000e+00 64289.40 0.000000e+00
## 4 JC+G(4)+I 65 -32223.44 64576.88 0.000000e+00 64577.40 0.000000e+00
## 3 JC+G(4) 64 -32237.07 64602.14 0.000000e+00 64602.65 0.000000e+00
## 2 JC+I 64 -32237.33 64602.66 0.000000e+00 64603.17 0.000000e+00
## 1 JC 63 -32775.40 65676.79 0.000000e+00 65677.29 0.000000e+00
## BIC
## 16 61137.58
## 15 61140.50
## 52 61142.14
## 44 61143.36
## 51 61145.77
## 24 61146.80
## 36 61146.83
## 43 61147.17
## 35 61149.86
## 23 61150.14
## 76 61151.39
## 68 61152.35
## 75 61155.38
## 60 61156.07
## 67 61156.86
## 84 61157.25
## 59 61159.49
## 83 61161.64
## 92 61166.27
## 91 61171.32
## 42 61261.53
## 14 61264.33
## 50 61267.14
## 66 61269.32
## 82 61272.63
## 22 61272.96
## 34 61273.77
## 74 61275.74
## 90 61280.40
## 58 61282.41
## 65 62606.99
## 41 62607.80
## 89 62621.84
## 81 62622.69
## 21 62658.29
## 13 62659.09
## 73 62664.93
## 49 62665.76
## 57 62667.99
## 33 62668.78
## 64 62690.93
## 88 62704.18
## 63 62716.18
## 87 62729.74
## 20 62735.60
## 72 62739.66
## 56 62745.28
## 62 62753.45
## 40 62753.99
## 19 62754.07
## 71 62758.82
## 39 62760.90
## 86 62763.30
## 55 62763.74
## 80 62766.96
## 79 62774.03
## 12 62789.39
## 11 62790.43
## 48 62793.14
## 47 62794.69
## 28 62799.04
## 32 62799.04
## 27 62800.04
## 31 62800.04
## 18 62820.14
## 70 62820.47
## 54 62829.83
## 38 62837.60
## 78 62847.57
## 10 62893.22
## 46 62893.82
## 26 62902.91
## 30 62902.91
## 8 63642.09
## 7 63655.61
## 6 63667.25
## 61 63905.00
## 85 63920.83
## 37 63980.58
## 77 63996.54
## 17 64023.66
## 69 64030.99
## 53 64033.37
## 9 64098.64
## 45 64106.03
## 25 64108.34
## 29 64108.34
## 5 64797.44
## 4 65077.75
## 3 65095.31
## 2 65095.83
## 1 66162.25
Meilleur modele: TPM3u+G(4)+I
env$`TPM3u+G(4)+I`
## pml(tree = `tree_TPM3u+G(4)+I`, data = data, bf = c(0.305879919520129,
## 0.277448712886181, 0.150392057313702, 0.266279310279987), Q = c(0.620577836420439,
## 16.6238593112725, 1, 0.620577836420439, 16.6238593112725, 1),
## model = "TPM3u", inv = 0.552749390092391, k = 4, shape = 1.18214235444543)
Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_5 = dist.logDet(mySequences_align_gr_ext_5_phangorn)
# Construction arbre NJ
treeNJ_gr_ext_5 <- NJ(mySequences_align_gr_ext_5)
# Visualisation
plot(treeNJ_gr_ext_5, main="Arbre NJ Groupe externe 5")
Integration des parametres
fit_gr_ext_5 = pml(treeNJ_gr_ext_5, data=mySequences_align_gr_ext_5_phangorn)
fitTPM3u_gr_ext_5 <- update(fit_gr_ext_5, model="TPM3u", k=4, inv=0.552855466228451, shape=1.18392191329267)
fitTPM3u_gr_ext_5 <- optim.pml(fitTPM3u_gr_ext_5, model="TPM3u", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_gr_ext_5 = bootstrap.pml(fitTPM3u_gr_ext_5, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTPM3u_gr_ext_5$tree), bs_gr_ext_5, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Alignement
mySequences_align_aa_gr_ext_5 = AlignTranslation(Sequences_groupe_externe_5,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)
## Determining distance matrix based on shared 6-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 1.12 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0.02 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.15 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 1.76 secs
Conversion
mySequences_align_aa_gr_ext_5_ape = as.AAbin(mySequences_align_aa_gr_ext_5)
mySequences_align_aa_gr_ext_5_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_5_ape, type = "AA")
## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.
Recherche du meilleur modele
mySequences_align_aa_gr_ext_5_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_5_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))
## Model df logLik AIC BIC
## WAG 63 -29719.28 59564.56 60002.67
## WAG+I 64 -29692.37 59512.74 59957.81
## WAG+G(4) 64 -29687.28 59502.55 59947.62
## WAG+G(4)+I 65 -29687.29 59504.58 59956.6
## JTT 63 -29599.93 59325.86 59763.98
## JTT+I 64 -29549.29 59226.58 59671.65
## JTT+G(4) 64 -29542.48 59212.95 59658.02
## JTT+G(4)+I 65 -29542.49 59214.99 59667.01
## LG 63 -29752.74 59631.49 60069.6
## LG+I 64 -29696.06 59520.13 59965.2
## LG+G(4) 64 -29684.48 59496.96 59942.03
## LG+G(4)+I 65 -29684.49 59498.97 59950.99
## Dayhoff 63 -30401.82 60929.64 61367.75
## Dayhoff+I 64 -30401.82 60931.64 61376.7
## Dayhoff+G(4) 64 -30402.21 60932.41 61377.48
## Dayhoff+G(4)+I 65 -30402.21 60934.41 61386.43
## cpREV 63 -29824.29 59774.59 60212.7
## cpREV+I 64 -29747.74 59623.49 60068.56
## cpREV+G(4) 64 -29743.66 59615.33 60060.39
## cpREV+G(4)+I 65 -29743.36 59616.72 60068.74
## mtmam 63 -30756.67 61639.35 62077.46
## mtmam+I 64 -30716.52 61561.05 62006.11
## mtmam+G(4) 64 -30715.03 61558.07 62003.13
## mtmam+G(4)+I 65 -30715.03 61560.05 62012.07
## mtArt 63 -29955.98 60037.97 60476.08
## mtArt+I 64 -29775.88 59679.76 60124.83
## mtArt+G(4) 64 -29727.75 59583.5 60028.57
## mtArt+G(4)+I 65 -29728.06 59586.12 60038.14
## MtZoa 63 -29889.03 59904.06 60342.18
## MtZoa+I 64 -29752.38 59632.76 60077.82
## MtZoa+G(4) 64 -29722.6 59573.19 60018.26
## MtZoa+G(4)+I 65 -29722.89 59575.77 60027.79
## mtREV24 63 -29416.38 58958.75 59396.87
## mtREV24+I 64 -29312.73 58753.47 59198.53
## mtREV24+G(4) 64 -29277.86 58683.73 59128.79
## mtREV24+G(4)+I 65 -29278.56 58687.11 59139.13
## VT 63 -29823.35 59772.69 60210.81
## VT+I 64 -29766.21 59660.42 60105.48
## VT+G(4) 64 -29742.01 59612.03 60057.09
## VT+G(4)+I 65 -29741.98 59613.97 60065.99
## RtREV 63 -29537.53 59201.06 59639.17
## RtREV+I 64 -29492.31 59112.63 59557.69
## RtREV+G(4) 64 -29482.59 59093.17 59538.24
## RtREV+G(4)+I 65 -29482.59 59095.18 59547.2
## HIVw 63 -30422.04 60970.09 61408.2
## HIVw+I 64 -30236.56 60601.13 61046.19
## HIVw+G(4) 64 -30209.78 60547.56 60992.63
## HIVw+G(4)+I 65 -30210.73 60551.46 61003.48
## HIVb 63 -29992.79 60111.59 60549.7
## HIVb+I 64 -29865.06 59858.11 60303.18
## HIVb+G(4) 64 -29854.96 59837.93 60282.99
## HIVb+G(4)+I 65 -29854.39 59838.79 60290.81
## FLU 63 -29565.76 59257.52 59695.63
## FLU+I 64 -29474.33 59076.66 59521.73
## FLU+G(4) 64 -30302.69 60733.38 61178.44
## FLU+G(4)+I 65 -29468.82 59067.65 59519.67
## Blosum62 63 -29757.08 59640.17 60078.28
## Blosum62+I 64 -29754.67 59637.34 60082.41
## Blosum62+G(4) 64 -29751.49 59630.97 60076.04
## Blosum62+G(4)+I 65 -29751.51 59633.02 60085.04
## Dayhoff_DCMut 63 -30398.14 60922.28 61360.39
## Dayhoff_DCMut+I 64 -30398.14 60924.28 61369.35
## Dayhoff_DCMut+G(4) 64 -30398.54 60925.08 61370.15
## Dayhoff_DCMut+G(4)+I 65 -30398.54 60927.08 61379.1
## JTT_DCMut 63 -29616.99 59359.98 59798.09
## JTT_DCMut+I 64 -29566.38 59260.76 59705.83
## JTT_DCMut+G(4) 64 -29559.78 59247.55 59692.62
## JTT_DCMut+G(4)+I 65 -29559.79 59249.59 59701.61
Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_5_modeltest, "env")
ls(env=env)
## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"
mySequences_align_aa_gr_ext_5_modeltest[order(mySequences_align_aa_gr_ext_5_modeltest$AIC), ]
## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 64 -29277.86 58683.73 8.443734e-01 58684.81
## 36 mtREV24+G(4)+I 65 -29278.56 58687.11 1.556266e-01 58688.23
## 34 mtREV24+I 64 -29312.73 58753.47 6.070336e-16 58754.55
## 33 mtREV24 63 -29416.38 58958.75 1.604746e-60 58959.80
## 56 FLU+G(4)+I 65 -29468.82 59067.65 3.623119e-84 59068.77
## 54 FLU+I 64 -29474.33 59076.66 4.000297e-86 59077.75
## 43 RtREV+G(4) 64 -29482.59 59093.17 1.039652e-89 59094.26
## 44 RtREV+G(4)+I 65 -29482.59 59095.18 3.803450e-90 59096.30
## 42 RtREV+I 64 -29492.31 59112.63 6.194778e-94 59113.71
## 41 RtREV 63 -29537.53 59201.06 3.892388e-113 59202.11
## 7 JTT+G(4) 64 -29542.48 59212.95 1.016163e-115 59214.04
## 8 JTT+G(4)+I 65 -29542.49 59214.99 3.671867e-116 59216.11
## 6 JTT+I 64 -29549.29 59226.58 1.116155e-118 59227.66
## 67 JTT_DCMut+G(4) 64 -29559.78 59247.55 3.114891e-123 59248.64
## 68 JTT_DCMut+G(4)+I 65 -29559.79 59249.59 1.125500e-123 59250.71
## 53 FLU 63 -29565.76 59257.52 2.137399e-125 59258.57
## 66 JTT_DCMut+I 64 -29566.38 59260.76 4.214858e-126 59261.85
## 5 JTT 63 -29599.93 59325.86 3.078524e-140 59326.92
## 65 JTT_DCMut 63 -29616.99 59359.98 1.204319e-147 59361.03
## 11 LG+G(4) 64 -29684.48 59496.96 2.159778e-177 59498.05
## 12 LG+G(4)+I 65 -29684.49 59498.97 7.921894e-178 59500.09
## 3 WAG+G(4) 64 -29687.28 59502.55 1.322408e-178 59503.64
## 4 WAG+G(4)+I 65 -29687.29 59504.58 4.785470e-179 59505.70
## 2 WAG+I 64 -29692.37 59512.74 8.091514e-181 59513.83
## 10 LG+I 64 -29696.06 59520.13 2.014807e-182 59521.21
## 1 WAG 63 -29719.28 59564.56 4.534831e-192 59565.61
## 31 MtZoa+G(4) 64 -29722.60 59573.19 6.047715e-194 59574.28
## 32 MtZoa+G(4)+I 65 -29722.89 59575.77 1.664165e-194 59576.89
## 27 mtArt+G(4) 64 -29727.75 59583.50 3.488603e-196 59584.59
## 28 mtArt+G(4)+I 65 -29728.06 59586.12 9.447127e-197 59587.23
## 39 VT+G(4) 64 -29742.01 59612.03 2.231969e-202 59613.11
## 40 VT+G(4)+I 65 -29741.98 59613.97 8.464233e-203 59615.09
## 19 cpREV+G(4) 64 -29743.66 59615.33 4.292618e-203 59616.41
## 20 cpREV+G(4)+I 65 -29743.36 59616.72 2.134880e-203 59617.84
## 18 cpREV+I 64 -29747.74 59623.49 7.242854e-205 59624.57
## 59 Blosum62+G(4) 64 -29751.49 59630.97 1.718260e-206 59632.06
## 9 LG 63 -29752.74 59631.49 1.327548e-206 59632.54
## 30 MtZoa+I 64 -29752.38 59632.76 7.041167e-207 59633.84
## 60 Blosum62+G(4)+I 65 -29751.51 59633.02 6.167908e-207 59634.14
## 58 Blosum62+I 64 -29754.67 59637.34 7.099579e-208 59638.43
## 57 Blosum62 63 -29757.08 59640.17 1.730959e-208 59641.22
## 38 VT+I 64 -29766.21 59660.42 6.931260e-213 59661.50
## 26 mtArt+I 64 -29775.88 59679.76 4.365891e-217 59680.85
## 37 VT 63 -29823.35 59772.69 2.888224e-237 59773.74
## 17 cpREV 63 -29824.29 59774.59 1.119339e-237 59775.64
## 51 HIVb+G(4) 64 -29854.96 59837.93 1.973936e-251 59839.01
## 52 HIVb+G(4)+I 65 -29854.39 59838.79 1.283383e-251 59839.91
## 50 HIVb+I 64 -29865.06 59858.11 8.168730e-256 59859.20
## 29 MtZoa 63 -29889.03 59904.06 8.591882e-266 59905.11
## 25 mtArt 63 -29955.98 60037.97 7.196560e-295 60039.02
## 49 HIVb 63 -29992.79 60111.59 7.422148e-311 60112.64
## 47 HIVw+G(4) 64 -30209.78 60547.56 0.000000e+00 60548.65
## 48 HIVw+G(4)+I 65 -30210.73 60551.46 0.000000e+00 60552.58
## 46 HIVw+I 64 -30236.56 60601.13 0.000000e+00 60602.21
## 55 FLU+G(4) 64 -30302.69 60733.38 0.000000e+00 60734.46
## 61 Dayhoff_DCMut 63 -30398.14 60922.28 0.000000e+00 60923.33
## 62 Dayhoff_DCMut+I 64 -30398.14 60924.28 0.000000e+00 60925.37
## 63 Dayhoff_DCMut+G(4) 64 -30398.54 60925.08 0.000000e+00 60926.16
## 64 Dayhoff_DCMut+G(4)+I 65 -30398.54 60927.08 0.000000e+00 60928.20
## 13 Dayhoff 63 -30401.82 60929.64 0.000000e+00 60930.69
## 14 Dayhoff+I 64 -30401.82 60931.64 0.000000e+00 60932.72
## 15 Dayhoff+G(4) 64 -30402.21 60932.41 0.000000e+00 60933.50
## 16 Dayhoff+G(4)+I 65 -30402.21 60934.41 0.000000e+00 60935.53
## 45 HIVw 63 -30422.04 60970.09 0.000000e+00 60971.14
## 23 mtmam+G(4) 64 -30715.03 61558.07 0.000000e+00 61559.15
## 24 mtmam+G(4)+I 65 -30715.03 61560.05 0.000000e+00 61561.17
## 22 mtmam+I 64 -30716.52 61561.05 0.000000e+00 61562.13
## 21 mtmam 63 -30756.67 61639.35 0.000000e+00 61640.40
## AICcw BIC
## 35 8.465957e-01 59128.79
## 36 1.534043e-01 59139.13
## 34 6.086313e-16 59198.53
## 33 1.636140e-60 59396.87
## 56 3.571382e-84 59519.67
## 54 4.010825e-86 59521.73
## 43 1.042388e-89 59538.24
## 44 3.749138e-90 59547.20
## 42 6.211082e-94 59557.69
## 41 3.968536e-113 59639.17
## 7 1.018837e-115 59658.02
## 8 3.619434e-116 59667.01
## 6 1.119092e-118 59671.65
## 67 3.123089e-123 59692.62
## 68 1.109428e-123 59701.61
## 53 2.179213e-125 59695.63
## 66 4.225951e-126 59705.83
## 5 3.138750e-140 59763.98
## 65 1.227880e-147 59798.09
## 11 2.165462e-177 59942.03
## 12 7.808773e-178 59950.99
## 3 1.325889e-178 59947.62
## 4 4.717135e-179 59956.60
## 2 8.112810e-181 59957.81
## 10 2.020110e-182 59965.20
## 1 4.623548e-192 60002.67
## 31 6.063632e-194 60018.26
## 32 1.640402e-194 60027.79
## 27 3.497785e-196 60028.57
## 28 9.312226e-197 60038.14
## 39 2.237843e-202 60057.09
## 40 8.343368e-203 60065.99
## 19 4.303916e-203 60060.39
## 20 2.104395e-203 60068.74
## 18 7.261916e-205 60068.56
## 59 1.722782e-206 60076.04
## 9 1.353519e-206 60069.60
## 30 7.059698e-207 60077.82
## 60 6.079833e-207 60085.04
## 58 7.118264e-208 60082.41
## 57 1.764822e-208 60078.28
## 38 6.949503e-213 60105.48
## 26 4.377381e-217 60124.83
## 37 2.944727e-237 60210.81
## 17 1.141237e-237 60212.70
## 51 1.979131e-251 60282.99
## 52 1.265056e-251 60290.81
## 50 8.190229e-256 60303.18
## 29 8.759968e-266 60342.18
## 25 7.337348e-295 60476.08
## 49 7.567350e-311 60549.70
## 47 0.000000e+00 60992.63
## 48 0.000000e+00 61003.48
## 46 0.000000e+00 61046.19
## 55 0.000000e+00 61178.44
## 61 0.000000e+00 61360.39
## 62 0.000000e+00 61369.35
## 63 0.000000e+00 61370.15
## 64 0.000000e+00 61379.10
## 13 0.000000e+00 61367.75
## 14 0.000000e+00 61376.70
## 15 0.000000e+00 61377.48
## 16 0.000000e+00 61386.43
## 45 0.000000e+00 61408.20
## 23 0.000000e+00 62003.13
## 24 0.000000e+00 62012.07
## 22 0.000000e+00 62006.11
## 21 0.000000e+00 62077.46
mySequences_align_aa_gr_ext_5_modeltest[order(mySequences_align_aa_gr_ext_5_modeltest$BIC), ]
## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 64 -29277.86 58683.73 8.443734e-01 58684.81
## 36 mtREV24+G(4)+I 65 -29278.56 58687.11 1.556266e-01 58688.23
## 34 mtREV24+I 64 -29312.73 58753.47 6.070336e-16 58754.55
## 33 mtREV24 63 -29416.38 58958.75 1.604746e-60 58959.80
## 56 FLU+G(4)+I 65 -29468.82 59067.65 3.623119e-84 59068.77
## 54 FLU+I 64 -29474.33 59076.66 4.000297e-86 59077.75
## 43 RtREV+G(4) 64 -29482.59 59093.17 1.039652e-89 59094.26
## 44 RtREV+G(4)+I 65 -29482.59 59095.18 3.803450e-90 59096.30
## 42 RtREV+I 64 -29492.31 59112.63 6.194778e-94 59113.71
## 41 RtREV 63 -29537.53 59201.06 3.892388e-113 59202.11
## 7 JTT+G(4) 64 -29542.48 59212.95 1.016163e-115 59214.04
## 8 JTT+G(4)+I 65 -29542.49 59214.99 3.671867e-116 59216.11
## 6 JTT+I 64 -29549.29 59226.58 1.116155e-118 59227.66
## 67 JTT_DCMut+G(4) 64 -29559.78 59247.55 3.114891e-123 59248.64
## 53 FLU 63 -29565.76 59257.52 2.137399e-125 59258.57
## 68 JTT_DCMut+G(4)+I 65 -29559.79 59249.59 1.125500e-123 59250.71
## 66 JTT_DCMut+I 64 -29566.38 59260.76 4.214858e-126 59261.85
## 5 JTT 63 -29599.93 59325.86 3.078524e-140 59326.92
## 65 JTT_DCMut 63 -29616.99 59359.98 1.204319e-147 59361.03
## 11 LG+G(4) 64 -29684.48 59496.96 2.159778e-177 59498.05
## 3 WAG+G(4) 64 -29687.28 59502.55 1.322408e-178 59503.64
## 12 LG+G(4)+I 65 -29684.49 59498.97 7.921894e-178 59500.09
## 4 WAG+G(4)+I 65 -29687.29 59504.58 4.785470e-179 59505.70
## 2 WAG+I 64 -29692.37 59512.74 8.091514e-181 59513.83
## 10 LG+I 64 -29696.06 59520.13 2.014807e-182 59521.21
## 1 WAG 63 -29719.28 59564.56 4.534831e-192 59565.61
## 31 MtZoa+G(4) 64 -29722.60 59573.19 6.047715e-194 59574.28
## 32 MtZoa+G(4)+I 65 -29722.89 59575.77 1.664165e-194 59576.89
## 27 mtArt+G(4) 64 -29727.75 59583.50 3.488603e-196 59584.59
## 28 mtArt+G(4)+I 65 -29728.06 59586.12 9.447127e-197 59587.23
## 39 VT+G(4) 64 -29742.01 59612.03 2.231969e-202 59613.11
## 19 cpREV+G(4) 64 -29743.66 59615.33 4.292618e-203 59616.41
## 40 VT+G(4)+I 65 -29741.98 59613.97 8.464233e-203 59615.09
## 18 cpREV+I 64 -29747.74 59623.49 7.242854e-205 59624.57
## 20 cpREV+G(4)+I 65 -29743.36 59616.72 2.134880e-203 59617.84
## 9 LG 63 -29752.74 59631.49 1.327548e-206 59632.54
## 59 Blosum62+G(4) 64 -29751.49 59630.97 1.718260e-206 59632.06
## 30 MtZoa+I 64 -29752.38 59632.76 7.041167e-207 59633.84
## 57 Blosum62 63 -29757.08 59640.17 1.730959e-208 59641.22
## 58 Blosum62+I 64 -29754.67 59637.34 7.099579e-208 59638.43
## 60 Blosum62+G(4)+I 65 -29751.51 59633.02 6.167908e-207 59634.14
## 38 VT+I 64 -29766.21 59660.42 6.931260e-213 59661.50
## 26 mtArt+I 64 -29775.88 59679.76 4.365891e-217 59680.85
## 37 VT 63 -29823.35 59772.69 2.888224e-237 59773.74
## 17 cpREV 63 -29824.29 59774.59 1.119339e-237 59775.64
## 51 HIVb+G(4) 64 -29854.96 59837.93 1.973936e-251 59839.01
## 52 HIVb+G(4)+I 65 -29854.39 59838.79 1.283383e-251 59839.91
## 50 HIVb+I 64 -29865.06 59858.11 8.168730e-256 59859.20
## 29 MtZoa 63 -29889.03 59904.06 8.591882e-266 59905.11
## 25 mtArt 63 -29955.98 60037.97 7.196560e-295 60039.02
## 49 HIVb 63 -29992.79 60111.59 7.422148e-311 60112.64
## 47 HIVw+G(4) 64 -30209.78 60547.56 0.000000e+00 60548.65
## 48 HIVw+G(4)+I 65 -30210.73 60551.46 0.000000e+00 60552.58
## 46 HIVw+I 64 -30236.56 60601.13 0.000000e+00 60602.21
## 55 FLU+G(4) 64 -30302.69 60733.38 0.000000e+00 60734.46
## 61 Dayhoff_DCMut 63 -30398.14 60922.28 0.000000e+00 60923.33
## 13 Dayhoff 63 -30401.82 60929.64 0.000000e+00 60930.69
## 62 Dayhoff_DCMut+I 64 -30398.14 60924.28 0.000000e+00 60925.37
## 63 Dayhoff_DCMut+G(4) 64 -30398.54 60925.08 0.000000e+00 60926.16
## 14 Dayhoff+I 64 -30401.82 60931.64 0.000000e+00 60932.72
## 15 Dayhoff+G(4) 64 -30402.21 60932.41 0.000000e+00 60933.50
## 64 Dayhoff_DCMut+G(4)+I 65 -30398.54 60927.08 0.000000e+00 60928.20
## 16 Dayhoff+G(4)+I 65 -30402.21 60934.41 0.000000e+00 60935.53
## 45 HIVw 63 -30422.04 60970.09 0.000000e+00 60971.14
## 23 mtmam+G(4) 64 -30715.03 61558.07 0.000000e+00 61559.15
## 22 mtmam+I 64 -30716.52 61561.05 0.000000e+00 61562.13
## 24 mtmam+G(4)+I 65 -30715.03 61560.05 0.000000e+00 61561.17
## 21 mtmam 63 -30756.67 61639.35 0.000000e+00 61640.40
## AICcw BIC
## 35 8.465957e-01 59128.79
## 36 1.534043e-01 59139.13
## 34 6.086313e-16 59198.53
## 33 1.636140e-60 59396.87
## 56 3.571382e-84 59519.67
## 54 4.010825e-86 59521.73
## 43 1.042388e-89 59538.24
## 44 3.749138e-90 59547.20
## 42 6.211082e-94 59557.69
## 41 3.968536e-113 59639.17
## 7 1.018837e-115 59658.02
## 8 3.619434e-116 59667.01
## 6 1.119092e-118 59671.65
## 67 3.123089e-123 59692.62
## 53 2.179213e-125 59695.63
## 68 1.109428e-123 59701.61
## 66 4.225951e-126 59705.83
## 5 3.138750e-140 59763.98
## 65 1.227880e-147 59798.09
## 11 2.165462e-177 59942.03
## 3 1.325889e-178 59947.62
## 12 7.808773e-178 59950.99
## 4 4.717135e-179 59956.60
## 2 8.112810e-181 59957.81
## 10 2.020110e-182 59965.20
## 1 4.623548e-192 60002.67
## 31 6.063632e-194 60018.26
## 32 1.640402e-194 60027.79
## 27 3.497785e-196 60028.57
## 28 9.312226e-197 60038.14
## 39 2.237843e-202 60057.09
## 19 4.303916e-203 60060.39
## 40 8.343368e-203 60065.99
## 18 7.261916e-205 60068.56
## 20 2.104395e-203 60068.74
## 9 1.353519e-206 60069.60
## 59 1.722782e-206 60076.04
## 30 7.059698e-207 60077.82
## 57 1.764822e-208 60078.28
## 58 7.118264e-208 60082.41
## 60 6.079833e-207 60085.04
## 38 6.949503e-213 60105.48
## 26 4.377381e-217 60124.83
## 37 2.944727e-237 60210.81
## 17 1.141237e-237 60212.70
## 51 1.979131e-251 60282.99
## 52 1.265056e-251 60290.81
## 50 8.190229e-256 60303.18
## 29 8.759968e-266 60342.18
## 25 7.337348e-295 60476.08
## 49 7.567350e-311 60549.70
## 47 0.000000e+00 60992.63
## 48 0.000000e+00 61003.48
## 46 0.000000e+00 61046.19
## 55 0.000000e+00 61178.44
## 61 0.000000e+00 61360.39
## 13 0.000000e+00 61367.75
## 62 0.000000e+00 61369.35
## 63 0.000000e+00 61370.15
## 14 0.000000e+00 61376.70
## 15 0.000000e+00 61377.48
## 64 0.000000e+00 61379.10
## 16 0.000000e+00 61386.43
## 45 0.000000e+00 61408.20
## 23 0.000000e+00 62003.13
## 22 0.000000e+00 62006.11
## 24 0.000000e+00 62012.07
## 21 0.000000e+00 62077.46
Meilleur modele : mtREV24+G(4)
env$`mtREV24+G(4)`
## pml(tree = `tree_mtREV24+G(4)`, data = data, model = "mtREV24",
## k = 4, shape = 0.552362280933957)
Construction arbres
# Matrice de ditance
dm_aa_gr_ext_5 <- dist.ml(mySequences_align_aa_gr_ext_5_phangorn, model = "mtREV24")
# Construction arbre NJ
treeNJ_aa_gr_ext_5 <- NJ(dm_aa_gr_ext_5)
Integration des parametres
fit_aa_gr_ext_5 = pml(treeNJ_aa_gr_ext_5, data=mySequences_align_aa_gr_ext_5_phangorn)
fitmtREV24_aa_gr_ext_5 <- update(fit_aa_gr_ext_5, model="mtREV24", shape = 0.55394324878572, k = 4)
fitmtREV24_aa_gr_ext_5 <- optim.pml(fitmtREV24_aa_gr_ext_5, model="mtREV24", optShape=TRUE, optGamma = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
Analyse bootstrap avec correction
bs_aa_gr_ext_5 = bootstrap.pml(fitmtREV24_aa_gr_ext_5, multicore=FALSE, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitmtREV24_aa_gr_ext_5$tree), bs_aa_gr_ext_5, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")